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.
42 ;; also sets up reftex for org-mode. The links are clickable and do
43 ;; things that are useful. You should really read org-ref.org for details.
45 ;; Package-Requires: ((dash))
49 The only external require is reftex-cite
51 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
52 (require 'reftex-cite)
57 There are some variables needed later to tell this library where you store your pdf files, where your notes file is, and your default bibliography. This variable is similar to the reftex-default-bibliography. I do not remember why I made it separate.
59 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
61 "customization group for org-ref")
63 (defcustom org-ref-bibliography-notes
65 "filename to where you will put all your notes about an entry in
66 the default bibliography."
70 (defcustom org-ref-default-bibliography
72 "list of bibtex files to search for. You should use full-paths for each file."
73 :type '(repeat :tag "List of bibtex files" file)
76 (defcustom org-ref-pdf-directory
78 "directory where pdfs are stored by key. put a trailing / in"
82 (defcustom org-ref-default-citation-link
84 "The default type of citation link to use"
88 (defcustom org-ref-insert-cite-key
90 "Keyboard shortcut to insert a citation."
94 (defcustom org-ref-bibliography-entry-format
95 '(("article" . "%a, %t, <i>%j</i>, <b>%v(%n)</b>, %p (%y). <a href=\"%U\">link</a>. <a href=\"http://dx.doi.org/%D\">doi</a>.")
97 ("book" . "%a, %t, %u (%y).")
99 ("proceedings" . "%e, %t in %S, %u (%y).")
101 ("inproceedings" . "%a, %t, %p, in %b, edited by %e, %u (%y)"))
103 "string to format an entry. Just the reference, no numbering at the beginning, etc... see the `org-ref-reftex-format-citation' docstring for the escape codes."
107 (defcustom org-ref-open-notes-function
113 ;;(org-tree-to-indirect-buffer)
114 (outline-previous-visible-heading 1)
115 (recenter-top-bottom 0))
116 "User-defined way to open a notes entry. This is excecuted after the entry is found, with the cursor at the beginning of the headline. The default setting fully expands the notes, and moves the headline to the top of the buffer")
119 This next variable determines the citation types that are available in org-ref. Links for each one are automatically generated, and completion functions are automatically generated. Users may add to this list in their own init files.
121 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
122 (defcustom org-ref-cite-types
123 '("cite" "nocite" ;; the default latex cite commands
124 ;; natbib cite commands, http://ctan.unixbrain.com/macros/latex/contrib/natbib/natnotes.pdf
125 "citet" "citet*" "citep" "citep*"
126 "citealt" "citealt*" "citealp" "citealp*"
128 "citeauthor" "citeauthor*"
129 "citeyear" "citeyear*"
130 "Citet" "Citep" "Citealt" "Citealp" "Citeauthor"
132 ;; http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf
134 "parencite" "Parencite"
135 "footcite" "footcitetext"
136 "textcite" "Textcite"
137 "smartcite" "Smartcite"
138 "cite*" "parencite*" "supercite"
139 "autocite" "Autocite" "autocite*" "Autocite*"
141 "citetitle" "citetitle*"
142 "citedate" "citedate*"
144 "fullcite" "footfullcite"
145 ;; "volcite" "Volcite" cannot support the syntax
146 "notecite" "Notecite"
147 "pnotecite" "Pnotecite"
149 ;; multicites. Very limited support for these.
150 "cites" "Cites" "parencites" "Parencites"
151 "footcites" "footcitetexts"
152 "smartcites" "Smartcites" "textcites" "Textcites"
153 "supercites" "autocites" "Autocites"
154 ;; for the bibentry package
157 "List of citation types known in org-ref"
158 :type '(repeat :tag "List of citation types" string)
162 We need a hook variable to store user-defined bibtex entry cleaning functions
163 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
164 (defcustom org-ref-clean-bibtex-entry-hook nil
165 "Hook that is run in org-ref-clean-bibtex-entry. The functions should take no arguments, and operate on the bibtex entry at point."
171 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
172 (defvar org-ref-bibliography-files
174 "variable to hold bibliography files to be searched")
177 ** org-mode / reftex setup
179 We setup reftex here. We use a custom insert cite link function defined here: [[*org-ref-insert-cite-link][org-ref-insert-cite-link]]. We setup reftex to use our org citation format.
181 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
183 (defun org-mode-reftex-setup ()
184 (and (buffer-file-name)
185 (file-exists-p (buffer-file-name))
186 (global-auto-revert-mode t)
187 ;; I do not remember why I put this next line in. It doesn't
188 ;; work for org-files. Nothing very bad happens, but it gives
189 ;; an annoying error. Commenting it out for now.
192 (make-local-variable 'reftex-cite-format)
193 (setq reftex-cite-format 'org)
194 (define-key org-mode-map (kbd org-ref-insert-cite-key) 'org-ref-insert-cite-link))
196 (add-hook 'org-mode-hook 'org-mode-reftex-setup)
198 (eval-after-load 'reftex-vars
200 (add-to-list 'reftex-cite-format-builtin
201 '(org "Org-mode citation"
202 ((?\C-m . "cite:%l") ; default
203 (?d . ",%l") ; for appending
209 (?h . "citeauthor:%l")
210 (?H . "citeauthor*:%l")
217 You may want to add new formats to the reftex-cite-format-builtin variable. Here is an example of adding two new formats. Note that this does not create the links.
219 #+BEGIN_SRC emacs-lisp :tangle no
221 (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
222 (append (nth 2 (assoc 'org reftex-cite-format-builtin)) '((?W . "textcite:%l")
223 (?z . "newcite:%l"))))
226 You can define a new citation link like this:
227 #+BEGIN_SRC emacs-lisp :tangle no
228 (org-ref-define-citation-link "citez" ?z)
232 Most of this library is the creation of functional links to help with references and citations.
234 We need several general utilities for this module. They are organized here. We frequently need to remove white space from the front and back of a string. Here we do that for a string.
236 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
237 (defun org-ref-strip-string (string)
238 "strip leading and trailing whitespace from the string"
239 (replace-regexp-in-string
240 (concat search-whitespace-regexp "$" ) ""
241 (replace-regexp-in-string
242 (concat "^" search-whitespace-regexp ) "" string)))
245 It is helpful to make the previous function operate on a list of strings here.
247 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
248 (defun org-ref-split-and-strip-string (string)
249 "split key-string and strip keys. Assumes the key-string is comma delimited"
250 (mapcar 'org-ref-strip-string (split-string string ",")))
253 ** bibliography and bibliographystyle
254 *** An html bibliography
256 Reftex is no longer being developed. I want a url and doi option for formatting, so I am modifying this [[file:emacs-24.3/lisp/textmodes/reftex-cite.el::(defun%20reftex-format-citation%20(entry%20format)][function]] from reftex-cite to provide that. We need to modify the reftex-get-bib-field code a bit to remove enclosing braces and quotes so we can make nice looking links.
258 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
259 (defun org-ref-reftex-get-bib-field (field entry &optional format)
260 "similar to reftex-get-bib-field, but removes enclosing braces and quotes"
262 (setq result (reftex-get-bib-field field entry format))
263 (when (and (not (string= result "")) (string= "{" (substring result 0 1)))
264 (setq result (substring result 1 -1)))
265 (when (and (not (string= result "")) (string= "\"" (substring result 0 1)))
266 (setq result (substring result 1 -1)))
269 (defun org-ref-reftex-format-citation (entry format)
270 "return a formatted string for the bibtex entry (from bibtex-parse-entry) according
271 to the format argument. The format is a string with these percent escapes.
273 In the format, the following percent escapes will be expanded.
275 %l The BibTeX label of the citation.
276 %a List of author names, see also `reftex-cite-punctuation'.
277 %2a Like %a, but abbreviate more than 2 authors like Jones et al.
278 %A First author name only.
279 %e Works like %a, but on list of editor names. (%2e and %E work a well)
281 It is also possible to access all other BibTeX database fields:
282 %b booktitle %c chapter %d edition %h howpublished
283 %i institution %j journal %k key %m month
284 %n number %o organization %p pages %P first page
285 %r address %s school %u publisher %t title
287 %B booktitle, abbreviated %T title, abbreviated
292 Usually, only %l is needed. The other stuff is mainly for the echo area
293 display, and for (setq reftex-comment-citations t).
295 %< as a special operator kills punctuation and space around it after the
296 string has been formatted.
298 A pair of square brackets indicates an optional argument, and RefTeX
299 will prompt for the values of these arguments.
301 Beware that all this only works with BibTeX database files. When
302 citations are made from the \bibitems in an explicit thebibliography
303 environment, only %l is available."
304 ;; Format a citation from the info in the BibTeX ENTRY
306 (unless (stringp format) (setq format "\\cite{%l}"))
308 (if (and reftex-comment-citations
309 (string-match "%l" reftex-cite-comment-format))
310 (error "reftex-cite-comment-format contains invalid %%l"))
313 "\\(\\`\\|[^%]\\)\\(\\(%\\([0-9]*\\)\\([a-zA-Z]\\)\\)[.,;: ]*\\)"
315 (let ((n (string-to-number (match-string 4 format)))
316 (l (string-to-char (match-string 5 format)))
322 (org-ref-reftex-get-bib-field "&key" entry)
323 (if reftex-comment-citations
324 reftex-cite-comment-format
326 ((= l ?a) (reftex-format-names
327 (reftex-get-bib-names "author" entry)
329 ((= l ?A) (car (reftex-get-bib-names "author" entry)))
330 ((= l ?b) (org-ref-reftex-get-bib-field "booktitle" entry "in: %s"))
331 ((= l ?B) (reftex-abbreviate-title
332 (org-ref-reftex-get-bib-field "booktitle" entry "in: %s")))
333 ((= l ?c) (org-ref-reftex-get-bib-field "chapter" entry))
334 ((= l ?d) (org-ref-reftex-get-bib-field "edition" entry))
335 ((= l ?D) (org-ref-reftex-get-bib-field "doi" entry))
336 ((= l ?e) (reftex-format-names
337 (reftex-get-bib-names "editor" entry)
339 ((= l ?E) (car (reftex-get-bib-names "editor" entry)))
340 ((= l ?h) (org-ref-reftex-get-bib-field "howpublished" entry))
341 ((= l ?i) (org-ref-reftex-get-bib-field "institution" entry))
342 ((= l ?j) (org-ref-reftex-get-bib-field "journal" entry))
343 ((= l ?k) (org-ref-reftex-get-bib-field "key" entry))
344 ((= l ?m) (org-ref-reftex-get-bib-field "month" entry))
345 ((= l ?n) (org-ref-reftex-get-bib-field "number" entry))
346 ((= l ?o) (org-ref-reftex-get-bib-field "organization" entry))
347 ((= l ?p) (org-ref-reftex-get-bib-field "pages" entry))
348 ((= l ?P) (car (split-string
349 (org-ref-reftex-get-bib-field "pages" entry)
351 ((= l ?s) (org-ref-reftex-get-bib-field "school" entry))
352 ((= l ?S) (org-ref-reftex-get-bib-field "series" entry))
353 ((= l ?u) (org-ref-reftex-get-bib-field "publisher" entry))
354 ((= l ?U) (org-ref-reftex-get-bib-field "url" entry))
355 ((= l ?r) (org-ref-reftex-get-bib-field "address" entry))
356 ;; strip enclosing brackets from title if they are there
357 ((= l ?t) (org-ref-reftex-get-bib-field "title" entry))
358 ((= l ?T) (reftex-abbreviate-title
359 (org-ref-reftex-get-bib-field "title" entry)))
360 ((= l ?v) (org-ref-reftex-get-bib-field "volume" entry))
361 ((= l ?y) (org-ref-reftex-get-bib-field "year" entry)))))
364 (setq b (match-beginning 2) e (match-end 2))
365 (setq b (match-beginning 3) e (match-end 3)))
366 (setq format (concat (substring format 0 b) rpl (substring format e)))))
367 (while (string-match "%%" format)
368 (setq format (replace-match "%" t t format)))
369 (while (string-match "[ ,.;:]*%<" format)
370 (setq format (replace-match "" t t format)))
371 ;; also replace carriage returns, tabs, and multiple whitespaces
372 (setq format (replace-regexp-in-string "\n\\|\t\\|\s+" " " format))
375 (defun org-ref-get-bibtex-entry-citation (key)
376 "returns a string for the bibliography entry corresponding to key, and formatted according to the type in `org-ref-bibliography-entry-format'"
378 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
379 (file) (entry) (bibtex-entry) (entry-type) (format))
381 (setq file (catch 'result
382 (loop for file in org-ref-bibliography-files do
383 (if (org-ref-key-in-file-p key (file-truename file))
385 (message "%s not found in %s" key (file-truename file))))))
388 (insert-file-contents file)
389 (bibtex-search-entry key nil 0)
390 (setq bibtex-entry (bibtex-parse-entry))
391 (setq entry-type (downcase (cdr (assoc "=type=" bibtex-entry))))
392 (setq format (cdr (assoc entry-type org-ref-bibliography-entry-format)))
394 (setq entry (org-ref-reftex-format-citation bibtex-entry format))
396 (bibtex-narrow-to-entry)
397 (setq entry (buffer-string)))))
402 : org-ref-reftex-format-citation
404 Here is how to use the function. You call it with point in an entry in a bibtex file.
406 #+BEGIN_SRC emacs-lisp :tangle no
407 (let((org-ref-bibliography-entry-format "%a, %t, <i>%j</i>, <b>%v(%n)</b>, %p (%y). <a href=\"%U\">link</a>. <a href=\"http://dx.doi.org/%D\">doi</a>."))
408 (org-ref-get-bibtex-entry-citation "armiento-2014-high"))
411 : Armiento, Kozinsky, Hautier, , Fornari \& Ceder, High-throughput screening of perovskite alloys for piezoelectric performance and thermodynamic stability, <i>Phys. Rev. B</i>, <b>89()</b>, 134103 (2014). <a href="http://link.aps.org/doi/10.1103/PhysRevB.89.134103">link</a>. <a href="http://dx.doi.org/10.1103/PhysRevB.89.134103">doi</a>.
413 I am not sure why full author names are not used.
415 This code provides some functions to generate a simple sorted bibliography in html. First we get all the keys in the buffer.
417 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
418 (defun org-ref-get-bibtex-keys ()
419 "return a list of unique keys in the buffer."
421 (org-element-map (org-element-parse-buffer) 'link
423 (let ((plist (nth 1 link)))
424 (when (-contains? org-ref-cite-types (plist-get plist ':type))
427 (org-ref-split-and-strip-string (plist-get plist ':path)))
428 (when (not (-contains? keys key))
429 (setq keys (append keys (list key)))))))))
430 ;; Sort keys alphabetically
431 (setq keys (cl-sort keys 'string-lessp :key 'downcase))
435 This function gets the html for one entry.
437 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
438 (defun org-ref-get-bibtex-entry-html (key)
439 "returns an html string for the bibliography entry corresponding to key"
441 (format "<li><a id=\"%s\">[%s] %s</a></li>" key key (org-ref-get-bibtex-entry-citation key)))
444 Now, we map over the whole list of keys, and the whole bibliography, formatted as an unordered list.
446 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
447 (defun org-ref-get-html-bibliography ()
448 "Create an html bibliography when there are keys"
449 (let ((keys (org-ref-get-bibtex-keys)))
451 (concat "<h1>Bibliography</h1>
453 (mapconcat (lambda (x) (org-ref-get-bibtex-entry-html x)) keys "\n")
457 I do not have plans to make a numbered bibliography with numbered citations anytime soon. This will require changing the way the citation links are exported, and keeping track of the numbers.
459 *** An org bibliography
460 You can export an org-file to an org-file or org-buffer (org-org-epxort-as-org). In this case, it would be useful convert the cite links to links to custom_ids, and the bibliography link to a first-level heading Bibliography with org-bibtex like headings for each entry. This code should enable this. Right now, it does not appear to work for org export though.
462 First, we get the string for a single entry.
463 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
464 (defun org-ref-get-bibtex-entry-org (key)
465 "returns an org string for the bibliography entry corresponding to key"
466 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
467 (file) (entry) (bibtex-entry) (entry-type) (format))
469 (setq file (catch 'result
470 (loop for file in org-ref-bibliography-files do
471 (if (org-ref-key-in-file-p key (file-truename file))
473 (message "%s not found in %s" key (file-truename file))))))
476 (insert-file-contents file)
477 (bibtex-search-entry key nil 0)
478 (setq entry (bibtex-parse-entry))
483 " (org-ref-reftex-get-bib-field "author" entry)
484 (org-ref-reftex-get-bib-field "title" entry)
485 (concat " :CUSTOM_ID: " (org-ref-reftex-get-bib-field "=key=" entry) "\n"
486 (mapconcat (lambda (element) (format " :%s: %s"
487 (upcase (car element))
493 Now, we loop over the keys, and combine all the entries into a bibliography.
494 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
495 (defun org-ref-get-org-bibliography ()
496 "Create an org bibliography when there are keys"
497 (let ((keys (org-ref-get-bibtex-keys)))
499 (concat "* Bibliography
501 (mapconcat (lambda (x) (org-ref-get-bibtex-entry-org x)) keys "\n")
505 *** An ascii bibliography
507 This function gets the html for one entry.
509 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
510 (defun org-ref-get-bibtex-entry-ascii (key)
511 "returns an ascii string for the bibliography entry corresponding to key"
513 (format "[%s] %s" key (org-ref-get-bibtex-entry-citation key)))
516 Now, we map over the whole list of keys, and the whole bibliography, formatted as an unordered list.
518 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
519 (defun org-ref-get-ascii-bibliography ()
520 "Create an html bibliography when there are keys"
521 (let ((keys (org-ref-get-bibtex-keys)))
527 (mapconcat (lambda (x) (org-ref-get-bibtex-entry-ascii x)) keys "\n")
533 We use a link for the bibliography so that we can click on it to open the bibliography file. The link may have more than one bibliography file in it, separated by commas. Clicking opens the file under the cursor. The bibliographies should be full filenames with the bib extension. Clicking on this link makes reftex-default-bibliography local and sets it to the list of files in the link. We need this to use reftex's searching capability.
535 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
536 (org-add-link-type "bibliography"
537 ;; this code is run on clicking. The bibliography
538 ;; may contain multiple files. this code finds the
539 ;; one you clicked on and opens it.
540 (lambda (link-string)
541 ;; get link-string boundaries
542 ;; we have to go to the beginning of the line, and then search forward
545 ;; object is the link you clicked on
546 (object (org-element-context))
548 (link-string-beginning)
552 (goto-char (org-element-property :begin object))
553 (search-forward link-string nil nil 1)
554 (setq link-string-beginning (match-beginning 0))
555 (setq link-string-end (match-end 0)))
557 ;; We set the reftex-default-bibliography
558 ;; here. it should be a local variable only in
559 ;; the current buffer. We need this for using
560 ;; reftex to do citations.
561 (set (make-local-variable 'reftex-default-bibliography)
562 (split-string (org-element-property :path object) ","))
564 ;; now if we have comma separated bibliographies
565 ;; we find the one clicked on. we want to
566 ;; search forward to next comma from point
568 (if (search-forward "," link-string-end 1 1)
569 (setq key-end (- (match-end 0) 1)) ; we found a match
570 (setq key-end (point)))) ; no comma found so take the point
571 ;; and backward to previous comma from point
573 (if (search-backward "," link-string-beginning 1 1)
574 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
575 (setq key-beginning (point)))) ; no match found
576 ;; save the key we clicked on.
577 (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
578 (find-file bibfile))) ; open file on click
581 (lambda (keyword desc format)
583 ((eq format 'org) (org-ref-get-org-bibliography))
584 ((eq format 'ascii) (org-ref-get-ascii-bibliography))
585 ((eq format 'html) (org-ref-get-html-bibliography))
587 ;; write out the latex bibliography command
588 (format "\\bibliography{%s}" (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
589 (mapcar 'expand-file-name
590 (split-string keyword ","))
595 Believe it or not, sometimes it makes sense /not/ to include the bibliography in a document (e.g. when you are required to submit references as a separate file). To generate the references, in another file, you must make a little tex file with these contents, and then compile it.
598 \input{project-description.bbl}
601 Here, we make a =nobibliography= link that acts like the bibliography, enables creation of the bbl file, but does not put an actual bibliography in the file.
603 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
604 (org-add-link-type "nobibliography"
605 ;; this code is run on clicking. The bibliography
606 ;; may contain multiple files. this code finds the
607 ;; one you clicked on and opens it.
608 (lambda (link-string)
609 ;; get link-string boundaries
610 ;; we have to go to the beginning of the line, and then search forward
613 ;; object is the link you clicked on
614 (object (org-element-context))
616 (link-string-beginning)
620 (goto-char (org-element-property :begin object))
621 (search-forward link-string nil nil 1)
622 (setq link-string-beginning (match-beginning 0))
623 (setq link-string-end (match-end 0)))
625 ;; We set the reftex-default-bibliography
626 ;; here. it should be a local variable only in
627 ;; the current buffer. We need this for using
628 ;; reftex to do citations.
629 (set (make-local-variable 'reftex-default-bibliography)
630 (split-string (org-element-property :path object) ","))
632 ;; now if we have comma separated bibliographies
633 ;; we find the one clicked on. we want to
634 ;; search forward to next comma from point
636 (if (search-forward "," link-string-end 1 1)
637 (setq key-end (- (match-end 0) 1)) ; we found a match
638 (setq key-end (point)))) ; no comma found so take the point
639 ;; and backward to previous comma from point
641 (if (search-backward "," link-string-beginning 1 1)
642 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
643 (setq key-beginning (point)))) ; no match found
644 ;; save the key we clicked on.
645 (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
646 (find-file bibfile))) ; open file on click
649 (lambda (keyword desc format)
651 ((eq format 'org) (org-ref-get-org-bibliography))
652 ((eq format 'ascii) (org-ref-get-ascii-bibliography))
653 ((eq format 'html) (org-ref-get-html-bibliography))
655 ;; write out the latex bibliography command
657 ; (format "{\\setbox0\\vbox{\\bibliography{%s}}}"
658 ; (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
659 ; (mapcar 'expand-file-name
660 ; (split-string keyword ","))
663 (format "\\nobibliography{%s}"
664 (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
665 (mapcar 'expand-file-name
666 (split-string keyword ","))
672 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
673 (org-add-link-type "printbibliography"
674 (lambda (arg) (message "Nothing implemented for clicking here."))
675 (lambda (keyword desc format)
677 ((eq format 'org) (org-ref-get-org-bibliography))
678 ((eq format 'html) (org-ref-get-html-bibliography))
680 ;; write out the biblatex bibliography command
681 "\\printbibliography"))
685 We also create a bibliographystyle link. There is nothing to do on clicking here, and we create it for consistency. This sets the style for latex export, so use something appropriate there, e.g. unsrt, plain, plainnat, ...
687 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
688 (org-add-link-type "bibliographystyle"
689 (lambda (arg) (message "Nothing implemented for clicking here."))
690 (lambda (keyword desc format)
693 ;; write out the latex bibliography command
694 (format "\\bibliographystyle{%s}" keyword)))))
697 *** Completion for bibliography link
700 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
701 (defun org-bibliography-complete-link (&optional arg)
702 (format "bibliography:%s" (read-file-name "enter file: " nil nil t)))
704 (defun org-ref-insert-bibliography-link ()
705 "insert a bibliography with completion"
707 (insert (org-bibliography-complete-link)))
711 This is apparently used for biblatex.
712 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
713 (org-add-link-type "addbibresource"
714 ;; this code is run on clicking. The addbibresource
715 ;; may contain multiple files. this code finds the
716 ;; one you clicked on and opens it.
717 (lambda (link-string)
718 ;; get link-string boundaries
719 ;; we have to go to the beginning of the line, and then search forward
722 ;; object is the link you clicked on
723 (object (org-element-context))
725 (link-string-beginning)
729 (goto-char (org-element-property :begin object))
730 (search-forward link-string nil nil 1)
731 (setq link-string-beginning (match-beginning 0))
732 (setq link-string-end (match-end 0)))
734 ;; We set the reftex-default-addbibresource
735 ;; here. it should be a local variable only in
736 ;; the current buffer. We need this for using
737 ;; reftex to do citations.
738 (set (make-local-variable 'reftex-default-addbibresource)
739 (split-string (org-element-property :path object) ","))
741 ;; now if we have comma separated bibliographies
742 ;; we find the one clicked on. we want to
743 ;; search forward to next comma from point
745 (if (search-forward "," link-string-end 1 1)
746 (setq key-end (- (match-end 0) 1)) ; we found a match
747 (setq key-end (point)))) ; no comma found so take the point
748 ;; and backward to previous comma from point
750 (if (search-backward "," link-string-beginning 1 1)
751 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
752 (setq key-beginning (point)))) ; no match found
753 ;; save the key we clicked on.
754 (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
755 (find-file bibfile))) ; open file on click
758 (lambda (keyword desc format)
760 ((eq format 'html) (format "")); no output for html
762 ;; write out the latex addbibresource command
763 (format "\\addbibresource{%s}" keyword)))))
768 In long documents, a list of figures is not uncommon. Here we create a clickable link that generates a temporary buffer containing a list of figures in the document, and their captions. We make a function that can be called interactively, and define a link type that is rendered in LaTeX to create the list of figures.
770 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
771 (defun org-ref-list-of-figures (&optional arg)
772 "Generate buffer with list of figures in them"
774 (save-excursion (widen)
775 (let* ((c-b (buffer-name))
778 (org-element-map (org-element-parse-buffer) 'link
780 "create a link for to the figure"
782 (and (string= (org-element-property :type link) "file")
784 "[^.]*\\.\\(png\\|jpg\\|eps\\|pdf\\)$"
785 (org-element-property :path link)))
788 (let* ((start (org-element-property :begin link))
789 (parent (car (cdr (org-element-property :parent link))))
790 (caption (caaar (plist-get parent :caption)))
791 (name (plist-get parent :name)))
794 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]] %s\n"
795 c-b start counter (or name "") caption)
797 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]]\n"
798 c-b start counter (or name "")))))))))
799 (switch-to-buffer "*List of Figures*")
800 (setq buffer-read-only nil)
803 (insert (mapconcat 'identity list-of-figures ""))
804 (setq buffer-read-only t)
805 (use-local-map (copy-keymap org-mode-map))
806 (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
810 'org-ref-list-of-figures ; on click
811 (lambda (keyword desc format)
814 (format "\\listoffigures")))))
819 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
820 (defun org-ref-list-of-tables (&optional arg)
821 "Generate a buffer with a list of tables"
825 (let* ((c-b (buffer-name))
828 (org-element-map (org-element-parse-buffer 'element) 'table
830 "create a link for to the table"
832 (let ((start (org-element-property :begin table))
833 (name (org-element-property :name table))
834 (caption (caaar (org-element-property :caption table))))
837 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]] %s\n"
838 c-b start counter (or name "") caption)
840 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]]\n"
841 c-b start counter (or name ""))))))))
842 (switch-to-buffer "*List of Tables*")
843 (setq buffer-read-only nil)
846 (insert (mapconcat 'identity list-of-tables ""))
847 (setq buffer-read-only t)
848 (use-local-map (copy-keymap org-mode-map))
849 (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
853 'org-ref-list-of-tables
854 (lambda (keyword desc format)
857 (format "\\listoftables")))))
861 The label link provides a way to create labels in org-mode. We make it clickable because we want to make sure labels are unique. This code will tell you how many instances of a label are found. We search for label links, LaTeX labels, and the org-mode format for labels. We probably should search for tblnames too.
862 *************** TODO search tblnames, custom_ids and check for case sensitivity
865 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
869 "on clicking count the number of label tags used in the buffer. A number greater than one means multiple labels!"
870 (message (format "%s occurences"
871 (+ (count-matches (format "label:%s\\b[^-:]" label) (point-min) (point-max) t)
872 ;; for tblname, it is not enough to get word boundary
873 ;; tab-little and tab-little-2 match then.
874 (count-matches (format "^#\\+tblname:\\s-*%s\\b[^-:]" label) (point-min) (point-max) t)
875 (count-matches (format "\\label{%s}\\b" label) (point-min) (point-max) t)
876 ;; this is the org-format #+label:
877 (count-matches (format "^#\\+label:\\s-*%s\\b[^-:]" label) (point-min) (point-max) t)))))
878 (lambda (keyword desc format)
880 ((eq format 'html) (format "(<label>%s</label>)" path))
882 (format "\\label{%s}" keyword)))))
885 We want to store links on labels, so you can put the cursor on the label, press C-c l, and later use C-c C-l to insert a link to the label. We also want to store links to tables with a table name, and for sections with CUSTOM_ID.
887 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
888 (defun org-label-store-link ()
889 "store a link to a label. The output will be a ref to that label"
890 ;; First we have to make sure we are on a label link.
891 (let* ((object (org-element-context)))
892 (when (and (equal (org-element-type object) 'link)
893 (equal (org-element-property :type object) "label"))
894 (org-store-link-props
896 :link (concat "ref:" (org-element-property :path object))))
898 ;; Store link on table
899 (when (equal (org-element-type object) 'table)
900 (org-store-link-props
902 :link (concat "ref:" (org-element-property :name object))))
904 ;; it turns out this does not work. you can already store a link to a heading with a CUSTOM_ID
905 ;; store link on heading with custom_id
906 ; (when (and (equal (org-element-type object) 'headline)
907 ; (org-entry-get (point) "CUSTOM_ID"))
908 ; (org-store-link-props
910 ; :link (concat "ref:" (org-entry-get (point) "CUSTOM_ID"))))
912 ;; and to #+label: lines
913 (when (and (equal (org-element-type object) 'paragraph)
914 (org-element-property :name object))
915 (org-store-link-props
917 :link (concat "ref:" (org-element-property :name object))))
920 (add-hook 'org-store-link-functions 'org-label-store-link)
924 The ref link allows you make links to labels. Clicking on the link takes you to the label, and provides a mark to go back to.
926 At the moment, ref links are not usable for section links. You need [[#CUSTOM_ID]] type links.
928 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
932 "on clicking goto the label. Navigate back with C-c &"
934 ;; next search from beginning of the buffer
936 ;; it is possible you would not find the label if narrowing is in effect
943 (goto-char (point-min))
944 (re-search-forward (format "label:%s\\b" label) nil t))
948 (goto-char (point-min))
949 (re-search-forward (format "\\label{%s}" label) nil t))
951 ;; #+label: name org-definition
953 (goto-char (point-min))
954 (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
958 (goto-char (point-min))
959 (re-search-forward (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t))
961 ;; Commented out because these ref links do not actually translate correctly in LaTeX.
962 ;; you need [[#label]] links.
965 ; (goto-char (point-min))
966 ; (re-search-forward (format ":CUSTOM_ID:\s-*\\(%s\\)" label) nil t))
968 ;; we did not find anything, so go back to where we came
970 (error "%s not found" label))
972 (message "go back with (org-mark-ring-goto) `C-c &`"))
974 (lambda (keyword desc format)
976 ((eq format 'html) (format "(<ref>%s</ref>)" path))
978 (format "\\ref{%s}" keyword)))))
981 It would be nice to use completion to enter a ref link, where a list of labels is provided. The following code searches the buffer for org and latex labels, custom_ids, and table names as potential items to make a ref link to.
983 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
984 (defun org-ref-get-org-labels ()
985 "find #+LABEL: labels"
987 (goto-char (point-min))
989 (while (re-search-forward "^#\\+label:\\s-+\\(.*\\)\\b" (point-max) t)
990 (add-to-list 'matches (match-string-no-properties 1) t))
994 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
995 (defun org-ref-get-custom-ids ()
996 "return a list of custom_id properties in the buffer"
997 (let ((results '()) custom_id)
1000 (let ((custom_id (org-entry-get (point) "CUSTOM_ID")))
1001 (when (not (null custom_id))
1002 (setq results (append results (list custom_id)))))))
1006 Here we get a list of the labels defined as raw latex labels, e.g. \label{eqtre}.
1007 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1008 (defun org-ref-get-latex-labels ()
1010 (goto-char (point-min))
1011 (let ((matches '()))
1012 (while (re-search-forward "\\\\label{\\([a-zA-z0-9:-]*\\)}" (point-max) t)
1013 (add-to-list 'matches (match-string-no-properties 1) t))
1017 Finally, we get the table names.
1019 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1020 (defun org-ref-get-tblnames ()
1021 (org-element-map (org-element-parse-buffer 'element) 'table
1023 (org-element-property :name table))))
1026 Now, we can put all the labels together which will give us a list of candidates.
1028 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1029 (defun org-ref-get-labels ()
1030 "returns a list of labels in the buffer that you can make a ref link to. this is used to auto-complete ref links."
1034 (goto-char (point-min))
1035 (let ((matches '()))
1036 (while (re-search-forward "label:\\([a-zA-z0-9:-]*\\)" (point-max) t)
1037 (add-to-list 'matches (match-string-no-properties 1) t))
1038 (append matches (org-ref-get-org-labels) (org-ref-get-latex-labels) (org-ref-get-tblnames) (org-ref-get-custom-ids))))))
1041 Now we create the completion function. This works from the org-machinery, e.g. if you type C-c C-l to insert a link, and use completion by pressing tab.
1043 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1044 (defun org-ref-complete-link (&optional arg)
1045 "Completion function for ref links"
1047 (setq label (completing-read "label: " (org-ref-get-labels)))
1048 (format "ref:%s" label)))
1051 Alternatively, you may want to just call a function that inserts a link with completion:
1053 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1054 (defun org-ref-insert-ref-link ()
1056 (insert (org-ref-complete-link)))
1061 This refers to the page of a label in LaTeX.
1063 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1067 "on clicking goto the label. Navigate back with C-c &"
1068 (org-mark-ring-push)
1069 ;; next search from beginning of the buffer
1075 (goto-char (point-min))
1076 (re-search-forward (format "label:%s\\b" label) nil t))
1080 (goto-char (point-min))
1081 (re-search-forward (format "\\label{%s}" label) nil t))
1083 ;; #+label: name org-definition
1085 (goto-char (point-min))
1086 (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1090 (goto-char (point-min))
1091 (re-search-forward (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t))
1093 ;; Commented out because these ref links do not actually translate correctly in LaTeX.
1094 ;; you need [[#label]] links.
1097 ; (goto-char (point-min))
1098 ; (re-search-forward (format ":CUSTOM_ID:\s-*\\(%s\\)" label) nil t))
1100 ;; we did not find anything, so go back to where we came
1101 (org-mark-ring-goto)
1102 (error "%s not found" label))
1103 (message "go back with (org-mark-ring-goto) `C-c &`"))
1105 (lambda (keyword desc format)
1107 ((eq format 'html) (format "(<pageref>%s</pageref>)" path))
1109 (format "\\pageref{%s}" keyword)))))
1112 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1113 (defun org-pageref-complete-link (&optional arg)
1114 "Completion function for ref links"
1116 (setq label (completing-read "label: " (org-ref-get-labels)))
1117 (format "ref:%s" label)))
1120 Alternatively, you may want to just call a function that inserts a link with completion:
1122 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1123 (defun org-pageref-insert-ref-link ()
1125 (insert (org-pageref-complete-link)))
1130 The nameref link allows you make links to the text of a section with a label. Clicking on the link takes you to the label, and provides a mark to go back to. This only works if you put a raw latex label in the headline.
1132 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1136 "on clicking goto the label. Navigate back with C-c &"
1137 (org-mark-ring-push)
1138 ;; next search from beginning of the buffer
1144 (goto-char (point-min))
1145 (re-search-forward (format "\\label{%s}" label) nil t))
1147 ;; we did not find anything, so go back to where we came
1148 (org-mark-ring-goto)
1149 (error "%s not found" label))
1150 (message "go back with (org-mark-ring-goto) `C-c &`"))
1152 (lambda (keyword desc format)
1154 ((eq format 'html) (format "(<nameref>%s</nameref>)" path))
1156 (format "\\nameref{%s}" keyword)))))
1160 This is just the LaTeX ref for equations. On export, the reference is enclosed in parentheses.
1162 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1166 "on clicking goto the label. Navigate back with C-c &"
1167 (org-mark-ring-push)
1168 ;; next search from beginning of the buffer
1170 (goto-char (point-min))
1173 ;; search forward for the first match
1175 (re-search-forward (format "label:%s" label) nil t)
1177 (re-search-forward (format "\\label{%s}" label) nil t)
1178 ;; #+label: name org-definition
1179 (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1180 (org-mark-ring-goto)
1181 (error "%s not found" label))
1182 (message "go back with (org-mark-ring-goto) `C-c &`"))
1184 (lambda (keyword desc format)
1186 ((eq format 'html) (format "(<eqref>%s</eqref>)" path))
1188 (format "\\eqref{%s}" keyword)))))
1192 This is the main reason this library exists. We want the following behavior. A cite link should be able to contain multiple bibtex keys. You should be able to click on the link, and get a brief citation of the entry for that key, and a menu of options to open the bibtex file, open a pdf if you have it, open your notes on the entry, or open a url if it exists. You should be able to insert new references onto an existing cite link, or create new ones easily. The following code implements these features.
1194 *** Implementing the click actions of cite
1196 **** Getting the key we clicked on
1197 The first thing we need is to get the bibtex key we clicked on.
1199 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1200 (defun org-ref-get-bibtex-key-under-cursor ()
1201 "returns key under the bibtex cursor. We search forward from
1202 point to get a comma, or the end of the link, and then backwards
1203 to get a comma, or the beginning of the link. that delimits the
1204 keyword we clicked on. We also strip the text properties."
1206 (let* ((object (org-element-context))
1207 (link-string (org-element-property :path object)))
1208 ;; you may click on the part before the citations. here we make
1209 ;; sure to move to the beginning so you get the first citation.
1211 (goto-char (org-element-property :begin object))
1212 (search-forward link-string (org-element-property :end object))
1213 (goto-char (match-beginning 0))
1214 ;; check if we clicked before the path and move as needed.
1215 (unless (< cp (point))
1218 (if (not (org-element-property :contents-begin object))
1219 ;; this means no description in the link
1221 ;; we need the link path start and end
1223 (goto-char (org-element-property :begin object))
1224 (search-forward link-string nil nil 1)
1225 (setq link-string-beginning (match-beginning 0))
1226 (setq link-string-end (match-end 0)))
1228 ;; The key is the text between commas, or the link boundaries
1230 (if (search-forward "," link-string-end t 1)
1231 (setq key-end (- (match-end 0) 1)) ; we found a match
1232 (setq key-end link-string-end))) ; no comma found so take the end
1233 ;; and backward to previous comma from point which defines the start character
1235 (if (search-backward "," link-string-beginning 1 1)
1236 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
1237 (setq key-beginning link-string-beginning))) ; no match found
1238 ;; save the key we clicked on.
1239 (setq bibtex-key (org-ref-strip-string (buffer-substring key-beginning key-end)))
1240 (set-text-properties 0 (length bibtex-key) nil bibtex-key)
1242 ;; link with description. assume only one key
1246 We also need to find which bibliography file that key is in. For that, we need to know which bibliography files are referred to in the file. If none are specified with a bibliography link, we use the default bibliography. This function searches for a bibliography link, and then the LaTeX bibliography link. We also consider the addbibresource link which is used with biblatex.
1248 **** Getting the bibliographies
1249 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1250 (defun org-ref-find-bibliography ()
1251 "find the bibliography in the buffer.
1252 This function sets and returns cite-bibliography-files, which is a list of files
1253 either from bibliography:f1.bib,f2.bib
1254 \bibliography{f1,f2}
1255 internal bibliographies
1257 falling back to what the user has set in org-ref-default-bibliography
1262 (goto-char (point-min))
1263 ;; look for a bibliography link
1264 (when (re-search-forward "\\<bibliography:\\([^\]\|\n]+\\)" nil t)
1265 (setq org-ref-bibliography-files
1266 (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
1267 (throw 'result org-ref-bibliography-files))
1270 ;; we did not find a bibliography link. now look for \bibliography
1271 (goto-char (point-min))
1272 (when (re-search-forward "\\\\bibliography{\\([^}]+\\)}" nil t)
1273 ;; split, and add .bib to each file
1274 (setq org-ref-bibliography-files
1275 (mapcar (lambda (x) (concat x ".bib"))
1276 (mapcar 'org-ref-strip-string
1277 (split-string (match-string 1) ","))))
1278 (throw 'result org-ref-bibliography-files))
1280 ;; no bibliography found. maybe we need a biblatex addbibresource
1281 (goto-char (point-min))
1282 ;; look for a bibliography link
1283 (when (re-search-forward "addbibresource:\\([^\]\|\n]+\\)" nil t)
1284 (setq org-ref-bibliography-files
1285 (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
1286 (throw 'result org-ref-bibliography-files))
1288 ;; we did not find anything. use defaults
1289 (setq org-ref-bibliography-files org-ref-default-bibliography)))
1291 ;; set reftex-default-bibliography so we can search
1292 (set (make-local-variable 'reftex-default-bibliography) org-ref-bibliography-files)
1293 org-ref-bibliography-files)
1296 **** Finding the bibliography file a key is in
1297 Now, we can see if an entry is in a file.
1299 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1300 (defun org-ref-key-in-file-p (key filename)
1301 "determine if the key is in the file"
1302 (interactive "skey: \nsFile: ")
1303 (save-current-buffer
1304 (let ((bibtex-files (list filename)))
1305 (bibtex-search-entry key t))))
1308 Finally, we want to know which file the key is in.
1310 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1311 (defun org-ref-get-bibtex-key-and-file (&optional key)
1312 "returns the bibtex key and file that it is in. If no key is provided, get one under point"
1314 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
1317 (setq key (org-ref-get-bibtex-key-under-cursor)))
1318 (setq file (catch 'result
1319 (loop for file in org-ref-bibliography-files do
1320 (if (org-ref-key-in-file-p key (file-truename file))
1321 (throw 'result file)))))
1325 **** convenience functions to act on citation at point
1327 :ID: af0b2a82-a7c9-4c08-9dac-09f93abc4a92
1329 We need some convenience functions to open act on the citation at point. These will get the pdf, open the url, or open the notes.
1331 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1332 (defun org-ref-open-pdf-at-point ()
1333 "open the pdf for bibtex key under point if it exists"
1335 (let* ((results (org-ref-get-bibtex-key-and-file))
1337 (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key)))
1338 (if (file-exists-p pdf-file)
1339 (org-open-file pdf-file)
1340 (message "no pdf found for %s" key))))
1343 (defun org-ref-open-url-at-point ()
1344 "open the url for bibtex key under point."
1346 (let* ((results (org-ref-get-bibtex-key-and-file))
1348 (bibfile (cdr results)))
1351 (insert-file-contents bibfile)
1352 (bibtex-search-entry key)
1353 ;; I like this better than bibtex-url which does not always find
1356 (let ((url (bibtex-autokey-get-field "url")))
1361 (let ((doi (bibtex-autokey-get-field "doi")))
1363 (if (string-match "^http" doi)
1365 (browse-url (format "http://dx.doi.org/%s" doi)))
1366 (throw 'done nil))))))))
1369 (defun org-ref-open-notes-at-point ()
1370 "open the notes for bibtex key under point."
1372 (let* ((results (org-ref-get-bibtex-key-and-file))
1374 (bibfile (cdr results)))
1377 (insert-file-contents bibfile)
1378 (bibtex-search-entry key)
1379 (org-ref-open-bibtex-notes)))))
1382 (defun org-ref-citation-at-point ()
1383 "give message of current citation at point"
1385 (let* ((cb (current-buffer))
1386 (results (org-ref-get-bibtex-key-and-file))
1388 (bibfile (cdr results)))
1389 (message "%s" (progn
1391 (insert-file-contents bibfile)
1392 (bibtex-search-entry key)
1393 (org-ref-bib-citation))))))
1396 (defun org-ref-open-citation-at-point ()
1397 "open bibtex file to key at point"
1399 (let* ((cb (current-buffer))
1400 (results (org-ref-get-bibtex-key-and-file))
1402 (bibfile (cdr results)))
1404 (bibtex-search-entry key)))
1407 **** the actual minibuffer menu
1408 Now, we create the menu. This is a rewrite of the cite action. This makes the function extendable by users.
1410 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1411 (defvar org-ref-cite-menu-funcs '()
1412 "Functions to run on cite click menu. Each entry is a list of (key menu-name function).
1413 The function must take no arguments and work on the key at point. Do not modify this variable, it is set to empty in the menu click function, and functions are conditionally added to it.")
1416 (defvar org-ref-user-cite-menu-funcs
1417 '(("C" "rossref" org-ref-crossref-at-point))
1418 "user-defined functions to run on bibtex key at point.")
1421 (defun org-ref-get-doi-at-point ()
1422 "Get doi for key at point."
1424 (let* ((results (org-ref-get-bibtex-key-and-file))
1426 (bibfile (cdr results)))
1429 (insert-file-contents bibfile)
1430 (bibtex-search-entry key)
1431 (bibtex-autokey-get-field "doi")
1432 ;; in case doi is a url, remove the url part.
1433 (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))))
1436 ;; functions that operate on key at point for click menu
1437 (defun org-ref-wos-at-point ()
1438 "open the doi in wos for bibtex key under point."
1440 (doi-utils-wos (org-ref-get-doi-at-point)))
1443 (defun org-ref-wos-citing-at-point ()
1444 "open the doi in wos citing articles for bibtex key under point."
1446 (doi-utils-wos-citing (org-ref-get-doi-at-point)))
1449 (defun org-ref-wos-related-at-point ()
1450 "open the doi in wos related articles for bibtex key under point."
1452 (doi-utils-wos-related (org-ref-get-doi-at-point)))
1455 (defun org-ref-google-scholar-at-point ()
1456 "open the doi in google scholar for bibtex key under point."
1458 (doi-utils-google-scholar (org-ref-get-doi-at-point)))
1461 (defun org-ref-pubmed-at-point ()
1462 "open the doi in pubmed for bibtex key under point."
1464 (doi-utils-pubmed (org-ref-get-doi-at-point)))
1467 (defun org-ref-crossref-at-point ()
1468 "open the doi in crossref for bibtex key under point."
1470 (doi-utils-crossref (org-ref-get-doi-at-point)))
1473 (defun org-ref-cite-onclick-minibuffer-menu (&optional link-string)
1474 "action when a cite link is clicked on.
1475 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."
1477 (let* ((results (org-ref-get-bibtex-key-and-file))
1479 (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
1480 (bibfile (cdr results))
1481 (url (save-excursion
1483 (insert-file-contents bibfile)
1484 (bibtex-search-entry key)
1485 (bibtex-autokey-get-field "url"))))
1486 (doi (save-excursion
1488 (insert-file-contents bibfile)
1489 (bibtex-search-entry key)
1490 ;; I like this better than bibtex-url which does not always find
1492 (bibtex-autokey-get-field "doi")))))
1494 (when (string= "" doi) (setq doi nil))
1495 (when (string= "" url) (setq url nil))
1496 (setq org-ref-cite-menu-funcs '())
1502 'org-ref-cite-menu-funcs
1503 '("o" "pen" org-ref-open-citation-at-point)))
1506 (when (file-exists-p pdf-file)
1508 'org-ref-cite-menu-funcs
1509 '("p" "df" org-ref-open-pdf-at-point) t))
1513 'org-ref-cite-menu-funcs
1514 '("n" "otes" org-ref-open-notes-at-point) t)
1519 'org-ref-cite-menu-funcs
1520 '("u" "rl" org-ref-open-url-at-point) t))
1525 'org-ref-cite-menu-funcs
1526 '("w" "os" org-ref-wos-at-point) t)
1529 'org-ref-cite-menu-funcs
1530 '("c" "iting" org-ref-wos-citing-at-point) t)
1533 'org-ref-cite-menu-funcs
1534 '("r" "elated" org-ref-wos-related-at-point) t)
1537 'org-ref-cite-menu-funcs
1538 '("g" "oogle scholar" org-ref-google-scholar-at-point) t)
1541 'org-ref-cite-menu-funcs
1542 '("P" "ubmed" org-ref-pubmed-at-point) t))
1544 ;; add user functions
1545 (dolist (tup org-ref-user-cite-menu-funcs)
1547 'org-ref-cite-menu-funcs
1552 'org-ref-cite-menu-funcs
1553 '("q" "uit" (lambda ())) t)
1555 ;; now we make a menu
1556 ;; construct menu string as a message
1559 (let* ((results (org-ref-get-bibtex-key-and-file))
1561 (bibfile (cdr results)))
1564 (insert-file-contents bibfile)
1565 (bibtex-search-entry key)
1566 (org-ref-bib-citation))))
1570 (concat "[" (elt tup 0) "]"
1572 org-ref-cite-menu-funcs "")))
1574 (let* ((input (read-char-exclusive))
1576 (char-to-string input) org-ref-cite-menu-funcs)))
1577 ;; now run the function (2nd element in choice)
1586 : org-ref-cite-onclick-minibuffer-menu
1588 *** A function to format a cite link
1590 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.
1592 #+BEGIN_SRC emacs-lisp :tangle no
1593 ;(defun org-ref-cite-link-format (keyword desc format)
1595 ; ((eq format 'html) (mapconcat (lambda (key) (format "<a name=\"#%s\">%s</a>" key key) (org-ref-split-and-strip-string keyword) ",")))
1596 ; ((eq format 'latex)
1597 ; (concat "\\cite" (when desc (format "[%s]" desc)) "{"
1598 ; (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
1602 *** The actual cite link
1603 Finally, we define the cite link. This is deprecated; the links are autogenerated later. This is here for memory.
1605 #+BEGIN_SRC emacs-lisp :tangle no
1608 ; 'org-ref-cite-onclick-minibuffer-menu
1609 ; 'org-ref-cite-link-format)
1612 *** Automatic definition of the cite links
1613 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.
1615 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1616 (defmacro org-ref-make-completion-function (type)
1617 `(defun ,(intern (format "org-%s-complete-link" type)) (&optional arg)
1623 (let ((bibtex-files (org-ref-find-bibliography)))
1624 (bibtex-global-key-alist))))))
1627 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.
1629 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1630 (defmacro org-ref-make-format-function (type)
1631 `(defun ,(intern (format "org-ref-format-%s" type)) (keyword desc format)
1636 (format "[[#%s][%s]]" key key))
1637 (org-ref-split-and-strip-string keyword) ","))
1644 (org-ref-split-and-strip-string keyword) ",") "]"))
1649 (format "<a href=\"#%s\">%s</a>" key key))
1650 (org-ref-split-and-strip-string keyword) ","))
1653 (if (string= (substring type -1) "s")
1654 ;; biblatex format for multicite commands, which all end in s. These are formated as \cites{key1}{key2}...
1655 (concat "\\" ,type (mapconcat (lambda (key) (format "{%s}" key))
1656 (org-ref-split-and-strip-string keyword) ""))
1658 (concat "\\" ,type (when desc (org-ref-format-citation-description desc)) "{"
1659 (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
1665 We create the links by mapping the function onto the list of defined link types.
1667 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1668 (defun org-ref-format-citation-description (desc)
1669 "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 ::."
1672 ((string-match "::" desc)
1673 (format "[%s][%s]" (car (setq results (split-string desc "::"))) (cadr results)))
1674 (t (format "[%s]" desc))))
1676 (defun org-ref-define-citation-link (type &optional key)
1677 "add a citation link for org-ref. With optional key, set the reftex binding. For example:
1678 (org-ref-define-citation-link \"citez\" ?z) will create a new citez link, with reftex key of z,
1679 and the completion function."
1680 (interactive "sCitation Type: \ncKey: ")
1682 ;; create the formatting function
1683 (eval `(org-ref-make-format-function ,type))
1688 'org-ref-cite-onclick-minibuffer-menu
1689 (quote ,(intern (format "org-ref-format-%s" type)))))
1691 ;; create the completion function
1692 (eval `(org-ref-make-completion-function ,type))
1694 ;; store new type so it works with adding citations, which checks
1695 ;; for existence in this list
1696 (add-to-list 'org-ref-cite-types type)
1698 ;; and finally if a key is specified, we modify the reftex menu
1700 (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
1701 (append (nth 2 (assoc 'org reftex-cite-format-builtin))
1702 `((,key . ,(concat type ":%l")))))))
1704 ;; create all the link types and their completion functions
1705 (mapcar 'org-ref-define-citation-link org-ref-cite-types)
1708 *** org-ref-insert-cite-link
1709 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.
1711 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1712 (defun org-ref-insert-cite-link (alternative-cite)
1713 "Insert a default citation link using reftex. If you are on a link, it
1714 appends to the end of the link, otherwise, a new link is
1715 inserted. Use a prefix arg to get a menu of citation types."
1717 (org-ref-find-bibliography)
1718 (let* ((object (org-element-context))
1719 (link-string-beginning (org-element-property :begin object))
1720 (link-string-end (org-element-property :end object))
1721 (path (org-element-property :path object)))
1723 (if (not alternative-cite)
1726 ;; case where we are in a link
1727 ((and (equal (org-element-type object) 'link)
1728 (-contains? org-ref-cite-types (org-element-property :type object)))
1729 (goto-char link-string-end)
1730 ;; sometimes there are spaces at the end of the link
1731 ;; this code moves point pack until no spaces are there
1732 (while (looking-back " ") (backward-char))
1733 (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
1735 ;; We are next to a link, and we want to append
1738 (and (equal (org-element-type (org-element-context)) 'link)
1739 (-contains? org-ref-cite-types (org-element-property :type (org-element-context)))))
1740 (while (looking-back " ") (backward-char))
1741 (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
1743 ;; insert fresh link
1746 (concat org-ref-default-citation-link
1748 (mapconcat 'identity (reftex-citation t) ",")))))
1750 ;; you pressed a C-u so we run this code
1756 : org-ref-insert-cite-link
1758 *** Completion in cite links
1759 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.
1761 #+BEGIN_SRC emacs-lisp :tangle no
1762 (defun org-cite-complete-link (&optional arg)
1763 "Completion function for cite links"
1765 org-ref-default-citation-link
1768 (let ((bibtex-files (org-ref-find-bibliography)))
1769 (bibtex-global-key-alist)))))
1772 Alternatively, you may shortcut the org-machinery with this command. You will be prompted for a citation type, and then offered key completion.
1774 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1775 (defun org-ref-insert-cite-with-completion (type)
1776 "Insert a cite link with completion"
1777 (interactive (list (ido-completing-read "Type: " org-ref-cite-types)))
1778 (insert (funcall (intern (format "org-%s-complete-link" type)))))
1781 ** Storing links to a bibtex entry
1782 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.
1784 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1785 (defun org-ref-store-bibtex-entry-link ()
1786 "Save a citation link to the current bibtex entry. Saves in the default link type."
1788 (let ((link (concat org-ref-default-citation-link
1791 (bibtex-beginning-of-entry)
1792 (reftex-get-bib-field "=key=" (bibtex-parse-entry))))))
1793 (message "saved %s" link)
1794 (push (list link) org-stored-links)
1795 (car org-stored-links)))
1799 org-ref minimally supports index entries. To make an index in a file, you should put in the LaTeX header these lines
1802 #+LATEX_HEADER: \usepackage{makeidx}
1803 #+LATEX_HEADER: \makeindex
1806 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.
1809 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.
1814 [[index:hello!Sam@\textsl{Sam}]]
1815 [[index:Lin@\textbf{Lin}]]
1816 [[index:Joe|textit]]
1817 [[index:Lin@\textbf{Lin}]]
1818 [[index:Peter|see {hello}]]
1819 [[index:Jen|seealso{Jenny}]]
1821 index:encodings!input!cp850
1823 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1829 (lambda (path desc format)
1832 (format "\\index{%s}" path)))))
1834 ;; this will generate a temporary index of entries in the file.
1838 (let ((*index-links* '())
1839 (*initial-letters* '()))
1842 (org-element-map (org-element-parse-buffer) 'link
1844 (let ((type (nth 0 link))
1845 (plist (nth 1 link)))
1847 (when (equal (plist-get plist ':type) "index")
1850 (cons (plist-get plist :path)
1852 "[[elisp:(progn (switch-to-buffer \"%s\") (goto-char %s))][%s]]"
1854 (plist-get plist :begin) ;; position of link
1855 ;; grab a description
1857 (goto-char (plist-get plist :begin))
1858 (if (thing-at-point 'sentence)
1860 (replace-regexp-in-string
1861 "\n" "" (thing-at-point 'sentence))
1862 ;; or call it a link
1866 (setq *index-links* (cl-sort *index-links* 'string-lessp :key 'car))
1868 ;; now first letters
1869 (dolist (link *index-links*)
1870 (add-to-list '*initial-letters* (substring (car link) 0 1) t))
1872 ;; now create the index
1873 (switch-to-buffer (get-buffer-create "*index*"))
1876 (insert "#+TITLE: Index\n\n")
1877 (dolist (letter *initial-letters*)
1878 (insert (format "* %s\n" (upcase letter)))
1879 ;; now process the links
1882 (string= letter (substring (car (car *index-links*)) 0 1)))
1883 (let ((link (pop *index-links*)))
1884 (insert (format "%s %s\n\n" (car link) (cdr link))))))
1885 (switch-to-buffer "*index*")))
1887 (lambda (path desc format)
1890 (format "\\printindex")))))
1894 | 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*)) |
1895 | lambda | (path desc format) | (cond ((eq format (quote latex)) (format \printindex))) |
1898 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.
1900 #+LATEX_HEADER: \usepackage{glossaries}
1901 #+LATEX_HEADER: \makeglossaries
1903 And at the end of the document put \makeglossaries.
1905 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
1908 nil ;; no follow action
1909 (lambda (path desc format)
1912 (format "\\newglossaryentry{%s}{%s}" path desc)))))
1918 nil ;; no follow action
1919 (lambda (path desc format)
1922 (format "\\gls{%s}" path)))))
1927 nil ;; no follow action
1928 (lambda (path desc format)
1931 (format "\\glspl{%s}" path)))))
1936 nil ;; no follow action
1937 (lambda (path desc format)
1940 (format "\\Gls{%s}" path)))))
1945 nil ;; no follow action
1946 (lambda (path desc format)
1949 (format "\\Glspl{%s}" path)))))
1953 | Glspl | nil | (lambda (path desc format) (cond ((eq format (quote latex)) (format \Glspl{%s} path)))) |
1954 | Gls | nil | (lambda (path desc format) (cond ((eq format (quote latex)) (format \Gls{%s} path)))) |
1955 | glspl | nil | (lambda (path desc format) (cond ((eq format (quote latex)) (format \glspl{%s} path)))) |
1956 | gls | nil | (lambda (path desc format) (cond ((eq format (quote latex)) (format \gls{%s} path)))) |
1957 | newglossaryentry | nil | (lambda (path desc format) (cond ((eq format (quote latex)) (format \newglossaryentry{%s}{%s} path desc)))) |
1958 | google | (lambda (link-string) (browse-url (format http://www.google.com/search?q=%s (url-hexify-string link-string)))) | nil |
1959 | ResearcherID | (lambda (link-string) (browse-url (format http://www.researcherid.com/rid/%s link-string))) | nil |
1960 | orcid | (lambda (link-string) (browse-url (format http://orcid.org/%s link-string))) | nil |
1961 | message | org-mac-message-open | nil |
1962 | mac-outlook | org-mac-outlook-message-open | nil |
1963 | skim | org-mac-skim-open | nil |
1964 | addressbook | org-mac-addressbook-item-open | nil |
1965 | x-together-item | org-mac-together-item-open | nil |
1966 | ans | (lambda (path) (let* ((fields (split-string path ::)) (label (nth 0 fields)) (data (nth 1 fields)) (data-file (format %s-%s.dat tq-userid label))) (let ((temp-file data-file) (temp-buffer (get-buffer-create (generate-new-buffer-name *temp file*)))) (unwind-protect (prog1 (save-current-buffer (set-buffer temp-buffer) (insert data)) (save-current-buffer (set-buffer temp-buffer) (write-region nil nil temp-file nil 0))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer)))) (mygit (format git add %s data-file)) (mygit (format git commit -m "%s" data-file)) (mygit git push origin master))) | nil |
1967 | mc | (lambda (link) (org-entry-put (point) ANSWER link) (save-restriction (save-excursion (org-narrow-to-subtree) (goto-char (point-max)) (if (bolp) nil (insert \n)) (insert (format # you chose %s link))))) | nil |
1968 | exercise | (lambda (arg) (tq-check-internet) (tq-get-assignment arg)) | nil |
1969 | solution | (lambda (label) (tq-check-internet) (let ((default-directory (file-name-as-directory (expand-file-name tq-root-directory)))) (if (file-exists-p solutions) nil (make-directory solutions)) (let ((default-directory (file-name-as-directory (expand-file-name solutions)))) (if (file-exists-p label) (progn (find-file (concat label / label .org)) (tq-update)) (mygit (format git clone %s@%s:solutions/%s tq-current-course tq-git-server label)) (find-file (concat label / label .org)))))) | nil |
1970 | assignment | (lambda (arg) (tq-check-internet) (tq-get-assignment arg)) | nil |
1971 | doi | doi-link-menu | nil |
1972 | bibentry | org-ref-cite-onclick-minibuffer-menu | org-ref-format-bibentry |
1973 | Autocites | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Autocites |
1974 | autocites | org-ref-cite-onclick-minibuffer-menu | org-ref-format-autocites |
1975 | supercites | org-ref-cite-onclick-minibuffer-menu | org-ref-format-supercites |
1976 | Textcites | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Textcites |
1977 | textcites | org-ref-cite-onclick-minibuffer-menu | org-ref-format-textcites |
1978 | Smartcites | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Smartcites |
1979 | smartcites | org-ref-cite-onclick-minibuffer-menu | org-ref-format-smartcites |
1980 | footcitetexts | org-ref-cite-onclick-minibuffer-menu | org-ref-format-footcitetexts |
1981 | footcites | org-ref-cite-onclick-minibuffer-menu | org-ref-format-footcites |
1982 | Parencites | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Parencites |
1983 | parencites | org-ref-cite-onclick-minibuffer-menu | org-ref-format-parencites |
1984 | Cites | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Cites |
1985 | cites | org-ref-cite-onclick-minibuffer-menu | org-ref-format-cites |
1986 | fnotecite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-fnotecite |
1987 | Pnotecite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Pnotecite |
1988 | pnotecite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-pnotecite |
1989 | Notecite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Notecite |
1990 | notecite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-notecite |
1991 | footfullcite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-footfullcite |
1992 | fullcite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-fullcite |
1993 | citeurl | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citeurl |
1994 | citedate* | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citedate* |
1995 | citedate | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citedate |
1996 | citetitle* | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citetitle* |
1997 | citetitle | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citetitle |
1998 | Citeauthor* | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Citeauthor* |
1999 | Autocite* | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Autocite* |
2000 | autocite* | org-ref-cite-onclick-minibuffer-menu | org-ref-format-autocite* |
2001 | Autocite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Autocite |
2002 | autocite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-autocite |
2003 | supercite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-supercite |
2004 | parencite* | org-ref-cite-onclick-minibuffer-menu | org-ref-format-parencite* |
2005 | cite* | org-ref-cite-onclick-minibuffer-menu | org-ref-format-cite* |
2006 | Smartcite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Smartcite |
2007 | smartcite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-smartcite |
2008 | Textcite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Textcite |
2009 | textcite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-textcite |
2010 | footcitetext | org-ref-cite-onclick-minibuffer-menu | org-ref-format-footcitetext |
2011 | footcite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-footcite |
2012 | Parencite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Parencite |
2013 | parencite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-parencite |
2014 | Cite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Cite |
2015 | Citeauthor | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Citeauthor |
2016 | Citealp | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Citealp |
2017 | Citealt | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Citealt |
2018 | Citep | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Citep |
2019 | Citet | org-ref-cite-onclick-minibuffer-menu | org-ref-format-Citet |
2020 | citeyear* | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citeyear* |
2021 | citeyear | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citeyear |
2022 | citeauthor* | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citeauthor* |
2023 | citeauthor | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citeauthor |
2024 | citetext | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citetext |
2025 | citenum | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citenum |
2026 | citealp* | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citealp* |
2027 | citealp | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citealp |
2028 | citealt* | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citealt* |
2029 | citealt | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citealt |
2030 | citep* | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citep* |
2031 | citep | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citep |
2032 | citet* | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citet* |
2033 | citet | org-ref-cite-onclick-minibuffer-menu | org-ref-format-citet |
2034 | nocite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-nocite |
2035 | cite | org-ref-cite-onclick-minibuffer-menu | org-ref-format-cite |
2036 | eqref | (lambda (label) on clicking goto the label. Navigate back with C-c & (org-mark-ring-push) (widen) (goto-char (point-min)) (if (or (re-search-forward (format label:%s label) nil t) (re-search-forward (format \label{%s} label) nil t) (re-search-forward (format ^#\+label:\s-*\(%s\)\b label) nil t)) nil (org-mark-ring-goto) (error %s not found label)) (message go back with (org-mark-ring-goto) `C-c &`)) | (lambda (keyword desc format) (cond ((eq format (quote html)) (format (<eqref>%s</eqref>) path)) ((eq format (quote latex)) (format \eqref{%s} keyword)))) |
2037 | nameref | (lambda (label) on clicking goto the label. Navigate back with C-c & (org-mark-ring-push) (widen) (if (or (progn (goto-char (point-min)) (re-search-forward (format \label{%s} label) nil t))) nil (org-mark-ring-goto) (error %s not found label)) (message go back with (org-mark-ring-goto) `C-c &`)) | (lambda (keyword desc format) (cond ((eq format (quote html)) (format (<nameref>%s</nameref>) path)) ((eq format (quote latex)) (format \nameref{%s} keyword)))) |
2038 | pageref | (lambda (label) on clicking goto the label. Navigate back with C-c & (org-mark-ring-push) (widen) (if (or (progn (goto-char (point-min)) (re-search-forward (format label:%s\b label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format \label{%s} label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format ^#\+label:\s-*\(%s\)\b label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format ^#\+tblname:\s-*\(%s\)\b label) nil t))) nil (org-mark-ring-goto) (error %s not found label)) (message go back with (org-mark-ring-goto) `C-c &`)) | (lambda (keyword desc format) (cond ((eq format (quote html)) (format (<pageref>%s</pageref>) path)) ((eq format (quote latex)) (format \pageref{%s} keyword)))) |
2039 | ref | (lambda (label) on clicking goto the label. Navigate back with C-c & (org-mark-ring-push) (widen) (if (or (progn (goto-char (point-min)) (re-search-forward (format label:%s\b label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format \label{%s} label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format ^#\+label:\s-*\(%s\)\b label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format ^#\+tblname:\s-*\(%s\)\b label) nil t))) nil (org-mark-ring-goto) (error %s not found label)) (org-show-entry) (message go back with (org-mark-ring-goto) `C-c &`)) | (lambda (keyword desc format) (cond ((eq format (quote html)) (format (<ref>%s</ref>) path)) ((eq format (quote latex)) (format \ref{%s} keyword)))) |
2040 | label | (lambda (label) on clicking count the number of label tags used in the buffer. A number greater than one means multiple labels! (message (format %s occurences (+ (count-matches (format label:%s\b[^-:] label) (point-min) (point-max) t) (count-matches (format ^#\+tblname:\s-*%s\b[^-:] label) (point-min) (point-max) t) (count-matches (format \label{%s}\b label) (point-min) (point-max) t) (count-matches (format ^#\+label:\s-*%s\b[^-:] label) (point-min) (point-max) t))))) | (lambda (keyword desc format) (cond ((eq format (quote html)) (format (<label>%s</label>) path)) ((eq format (quote latex)) (format \label{%s} keyword)))) |
2041 | list-of-tables | org-ref-list-of-tables | (lambda (keyword desc format) (cond ((eq format (quote latex)) (format \listoftables)))) |
2042 | list-of-figures | org-ref-list-of-figures | (lambda (keyword desc format) (cond ((eq format (quote latex)) (format \listoffigures)))) |
2043 | addbibresource | (lambda (link-string) (let* ((bibfile) (object (org-element-context)) (link-string-beginning) (link-string-end)) (save-excursion (goto-char (org-element-property :begin object)) (search-forward link-string nil nil 1) (setq link-string-beginning (match-beginning 0)) (setq link-string-end (match-end 0))) (set (make-local-variable (quote reftex-default-addbibresource)) (split-string (org-element-property :path object) ,)) (save-excursion (if (search-forward , link-string-end 1 1) (setq key-end (- (match-end 0) 1)) (setq key-end (point)))) (save-excursion (if (search-backward , link-string-beginning 1 1) (setq key-beginning (+ (match-beginning 0) 1)) (setq key-beginning (point)))) (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end))) (find-file bibfile))) | (lambda (keyword desc format) (cond ((eq format (quote html)) (format )) ((eq format (quote latex)) (format \addbibresource{%s} keyword)))) |
2044 | bibliographystyle | (lambda (arg) (message Nothing implemented for clicking here.)) | (lambda (keyword desc format) (cond ((eq format (quote latex)) (format \bibliographystyle{%s} keyword)))) |
2045 | printbibliography | (lambda (arg) (message Nothing implemented for clicking here.)) | (lambda (keyword desc format) (cond ((eq format (quote org)) (org-ref-get-org-bibliography)) ((eq format (quote html)) (org-ref-get-html-bibliography)) ((eq format (quote latex)) \printbibliography))) |
2046 | nobibliography | (lambda (link-string) (let* ((bibfile) (object (org-element-context)) (link-string-beginning) (link-string-end)) (save-excursion (goto-char (org-element-property :begin object)) (search-forward link-string nil nil 1) (setq link-string-beginning (match-beginning 0)) (setq link-string-end (match-end 0))) (set (make-local-variable (quote reftex-default-bibliography)) (split-string (org-element-property :path object) ,)) (save-excursion (if (search-forward , link-string-end 1 1) (setq key-end (- (match-end 0) 1)) (setq key-end (point)))) (save-excursion (if (search-backward , link-string-beginning 1 1) (setq key-beginning (+ (match-beginning 0) 1)) (setq key-beginning (point)))) (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end))) (find-file bibfile))) | (lambda (keyword desc format) (cond ((eq format (quote org)) (org-ref-get-org-bibliography)) ((eq format (quote ascii)) (org-ref-get-ascii-bibliography)) ((eq format (quote html)) (org-ref-get-html-bibliography)) ((eq format (quote latex)) (format \nobibliography{%s} (replace-regexp-in-string \.bib (mapconcat (quote identity) (mapcar (quote expand-file-name) (split-string keyword ,)) ,)))))) |
2047 | bibliography | (lambda (link-string) (let* ((bibfile) (object (org-element-context)) (link-string-beginning) (link-string-end)) (save-excursion (goto-char (org-element-property :begin object)) (search-forward link-string nil nil 1) (setq link-string-beginning (match-beginning 0)) (setq link-string-end (match-end 0))) (set (make-local-variable (quote reftex-default-bibliography)) (split-string (org-element-property :path object) ,)) (save-excursion (if (search-forward , link-string-end 1 1) (setq key-end (- (match-end 0) 1)) (setq key-end (point)))) (save-excursion (if (search-backward , link-string-beginning 1 1) (setq key-beginning (+ (match-beginning 0) 1)) (setq key-beginning (point)))) (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end))) (find-file bibfile))) | (lambda (keyword desc format) (cond ((eq format (quote org)) (org-ref-get-org-bibliography)) ((eq format (quote ascii)) (org-ref-get-ascii-bibliography)) ((eq format (quote html)) (org-ref-get-html-bibliography)) ((eq format (quote latex)) (format \bibliography{%s} (replace-regexp-in-string \.bib (mapconcat (quote identity) (mapcar (quote expand-file-name) (split-string keyword ,)) ,)))))) |
2048 | rmail | org-rmail-open | nil |
2049 | mhe | org-mhe-open | nil |
2050 | irc | org-irc-visit | nil |
2051 | info | org-info-open | nil |
2052 | gnus | org-gnus-open | nil |
2053 | docview | org-docview-open | org-docview-export |
2054 | bibtex | org-bibtex-open | nil |
2055 | bbdb | org-bbdb-open | org-bbdb-export |
2056 | pydoc | (lambda (link-string) (shell-command (format python -m pydoc %s link-string))) | nil |
2057 | index | (lambda (path) (tq-index) (occur path)) | nil |
2058 | attachfile | (lambda (link-string) (org-open-file link-string)) | (lambda (keyword desc format) (cond ((eq format (quote html)) (format )) ((eq format (quote latex)) (format \attachfile{%s} keyword)))) |
2059 | msx | org-msx-open | nil |
2060 | id | org-id-open | nil |
2061 | file+emacs | org-open-file-with-emacs | nil |
2062 | file+sys | org-open-file-with-system | nil |
2067 ** create simple text citation from bibtex entry
2069 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2070 (defun org-ref-bib-citation ()
2071 "from a bibtex entry, create and return a simple citation string."
2073 (bibtex-beginning-of-entry)
2074 (let* ((cb (current-buffer))
2075 (bibtex-expand-strings t)
2076 (entry (loop for (key . value) in (bibtex-parse-entry t)
2077 collect (cons (downcase key) value)))
2078 (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2079 (year (reftex-get-bib-field "year" entry))
2080 (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2081 (key (reftex-get-bib-field "=key=" entry))
2082 (journal (reftex-get-bib-field "journal" entry))
2083 (volume (reftex-get-bib-field "volume" entry))
2084 (pages (reftex-get-bib-field "pages" entry))
2085 (doi (reftex-get-bib-field "doi" entry))
2086 (url (reftex-get-bib-field "url" entry))
2088 ;;authors, "title", Journal, vol(iss):pages (year).
2089 (format "%s, \"%s\", %s, %s:%s (%s)"
2090 author title journal volume pages year)))
2094 : org-ref-bib-citation
2097 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2098 (defun org-ref-bib-html-citation ()
2099 "from a bibtex entry, create and return a simple citation with html links."
2101 (bibtex-beginning-of-entry)
2102 (let* ((cb (current-buffer))
2103 (bibtex-expand-strings t)
2104 (entry (loop for (key . value) in (bibtex-parse-entry t)
2105 collect (cons (downcase key) value)))
2106 (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2107 (year (reftex-get-bib-field "year" entry))
2108 (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2109 (key (reftex-get-bib-field "=key=" entry))
2110 (journal (reftex-get-bib-field "journal" entry))
2111 (volume (reftex-get-bib-field "volume" entry))
2112 (pages (reftex-get-bib-field "pages" entry))
2113 (doi (reftex-get-bib-field "doi" entry))
2114 (url (reftex-get-bib-field "url" entry))
2116 ;;authors, "title", Journal, vol(iss):pages (year).
2117 (concat (format "%s, \"%s\", %s, %s:%s (%s)."
2118 author title journal volume pages year)
2119 (when url (format " <a href=\"%s\">link</a>" url))
2120 (when doi (format " <a href=\"http://dx.doi.org/%s\">doi</a>" doi)))
2124 ** open pdf from bibtex
2125 We bind this to a key here: [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2126 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2127 (defun org-ref-open-bibtex-pdf ()
2128 "open pdf for a bibtex entry, if it exists. assumes point is in
2129 the entry of interest in the bibfile. but does not check that."
2132 (bibtex-beginning-of-entry)
2133 (let* ((bibtex-expand-strings t)
2134 (entry (bibtex-parse-entry t))
2135 (key (reftex-get-bib-field "=key=" entry))
2136 (pdf (format (concat org-ref-pdf-directory "%s.pdf") key)))
2138 (if (file-exists-p pdf)
2139 (org-open-link-from-string (format "[[file:%s]]" pdf))
2143 ** open notes from bibtex
2144 We bind this to a key here [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2146 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2147 (defun org-ref-open-bibtex-notes ()
2148 "from a bibtex entry, open the notes if they exist, and create a heading if they do not.
2150 I never did figure out how to use reftex to make this happen
2151 non-interactively. the reftex-format-citation function did not
2152 work perfectly; there were carriage returns in the strings, and
2153 it did not put the key where it needed to be. so, below I replace
2154 the carriage returns and extra spaces with a single space and
2155 construct the heading by hand."
2158 (bibtex-beginning-of-entry)
2159 (let* ((cb (current-buffer))
2160 (bibtex-expand-strings t)
2161 (entry (loop for (key . value) in (bibtex-parse-entry t)
2162 collect (cons (downcase key) value)))
2163 (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2164 (year (reftex-get-bib-field "year" entry))
2165 (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2166 (key (reftex-get-bib-field "=key=" entry))
2167 (journal (reftex-get-bib-field "journal" entry))
2168 (volume (reftex-get-bib-field "volume" entry))
2169 (pages (reftex-get-bib-field "pages" entry))
2170 (doi (reftex-get-bib-field "doi" entry))
2171 (url (reftex-get-bib-field "url" entry))
2174 ;; save key to clipboard to make saving pdf later easier by pasting.
2177 (kill-ring-save (point-min) (point-max)))
2179 ;; now look for entry in the notes file
2180 (if org-ref-bibliography-notes
2181 (find-file-other-window org-ref-bibliography-notes)
2182 (error "org-ref-bib-bibliography-notes is not set to anything"))
2184 (goto-char (point-min))
2185 ;; put new entry in notes if we don't find it.
2186 (if (re-search-forward (format ":Custom_ID: %s$" key) nil 'end)
2187 (funcall org-ref-open-notes-function)
2188 ;; no entry found, so add one
2189 (insert (format "\n** TODO %s - %s" year title))
2201 [[cite:%s]] [[file:%s/%s.pdf][pdf]]\n\n"
2202 key author journal year volume pages doi url key org-ref-pdf-directory key))
2206 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2207 (defun org-ref-open-notes-from-reftex ()
2208 "Call reftex, and open notes for selected entry."
2210 (let ((bibtex-key )))
2212 ;; now look for entry in the notes file
2213 (if org-ref-bibliography-notes
2214 (find-file-other-window org-ref-bibliography-notes)
2215 (error "org-ref-bib-bibliography-notes is not set to anything"))
2217 (goto-char (point-min))
2219 (re-search-forward (format
2221 (first (reftex-citation t)) nil 'end))
2222 (funcall org-ref-open-notes-function))
2225 ** open url in browser from bibtex
2227 We bind this to a key here [[*key%20bindings%20for%20utilities][key bindings for utilities]].
2229 + 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.
2231 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2232 (defun org-ref-open-in-browser ()
2233 "Open the bibtex entry at point in a browser using the url field or doi field"
2236 (bibtex-beginning-of-entry)
2238 (let ((url (bibtex-autokey-get-field "url")))
2243 (let ((doi (bibtex-autokey-get-field "doi")))
2245 (if (string-match "^http" doi)
2247 (browse-url (format "http://dx.doi.org/%s" doi)))
2249 (message "No url or doi found"))))
2253 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.
2255 *** function to upload bibtex to citeulike
2257 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2258 (defun org-ref-upload-bibtex-entry-to-citeulike ()
2259 "with point in a bibtex entry get bibtex string and submit to citeulike.
2261 Relies on the python script /upload_bibtex_citeulike.py being in the user directory."
2263 (message "uploading to citeulike")
2265 (bibtex-narrow-to-entry)
2266 (let ((startpos (point-min))
2267 (endpos (point-max))
2268 (bibtex-string (buffer-string))
2269 (script (concat "python " starter-kit-dir "/upload_bibtex_citeulike.py&")))
2270 (with-temp-buffer (insert bibtex-string)
2271 (shell-command-on-region (point-min) (point-max) script t nil nil t)))))
2274 *** The upload script
2275 Here is the python script for uploading.
2277 *************** TODO document how to get the cookies
2281 #+BEGIN_SRC python :tangle upload_bibtex_citeulike.py
2283 import pickle, requests, sys
2286 with open('c:/Users/jkitchin/Dropbox/blogofile-jkitchin.github.com/_blog/cookies.pckl', 'rb') as f:
2287 cookies = pickle.load(f)
2289 url = 'http://www.citeulike.org/profile/jkitchin/import_do'
2291 bibtex = sys.stdin.read()
2293 data = {'pasted':bibtex,
2295 'tag_parsing':'simple',
2296 'strip_brackets':'no',
2297 'update_id':'bib-key',
2298 'btn_bibtex':'Import BibTeX file ...'}
2300 headers = {'content-type': 'multipart/form-data',
2301 'User-Agent':'jkitchin/johnrkitchin@gmail.com bibtexupload'}
2303 r = requests.post(url, headers=headers, data=data, cookies=cookies, files={})
2307 ** Build a pdf from a bibtex file
2308 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.
2310 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2311 (defun org-ref-build-full-bibliography ()
2312 "build pdf of all bibtex entries, and open it."
2314 (let* ((bibfile (file-name-nondirectory (buffer-file-name)))
2315 (bib-base (file-name-sans-extension bibfile))
2316 (texfile (concat bib-base ".tex"))
2317 (pdffile (concat bib-base ".pdf")))
2320 (insert (format "\\documentclass[12pt]{article}
2321 \\usepackage[version=3]{mhchem}
2323 \\usepackage[numbers]{natbib}
2324 \\usepackage[colorlinks=true, linkcolor=blue, urlcolor=blue, pdfstartview=FitH]{hyperref}
2328 \\bibliographystyle{unsrtnat}
2330 \\end{document}" bib-base))
2332 (shell-command (concat "pdflatex " bib-base))
2333 (shell-command (concat "bibtex " bib-base))
2334 (shell-command (concat "pdflatex " bib-base))
2335 (shell-command (concat "pdflatex " bib-base))
2336 (kill-buffer texfile)
2337 (org-open-file pdffile)
2341 ** Extract bibtex entries cited in an org-file
2342 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.
2344 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2345 (defun org-ref-extract-bibtex-entries ()
2346 "extract the bibtex entries referred to by cite links in the current buffer into a src block at the bottom of the current buffer.
2348 If no bibliography is in the buffer the `reftex-default-bibliography' is used."
2350 (let* ((temporary-file-directory (file-name-directory (buffer-file-name)))
2351 (tempname (make-temp-file "extract-bib"))
2352 (contents (buffer-string))
2353 (cb (current-buffer))
2354 basename texfile bibfile results)
2356 ;; open tempfile and insert org-buffer contents
2357 (find-file tempname)
2359 (setq basename (file-name-sans-extension
2360 (file-name-nondirectory buffer-file-name))
2361 texfile (concat tempname ".tex")
2362 bibfile (concat tempname ".bib"))
2364 ;; see if we have a bibliography, and insert the default one if not.
2366 (goto-char (point-min))
2367 (unless (re-search-forward "^bibliography:" (point-max) 'end)
2368 (insert (format "\nbibliography:%s"
2369 (mapconcat 'identity reftex-default-bibliography ",")))))
2372 ;; get a latex file and extract the references
2373 (org-latex-export-to-latex)
2376 (reftex-create-bibtex-file bibfile)
2378 ;; save results of the references
2379 (setq results (buffer-string))
2381 ;; kill buffers. these are named by basename, not full path
2382 (kill-buffer (concat basename ".bib"))
2383 (kill-buffer (concat basename ".tex"))
2384 (kill-buffer basename)
2386 (delete-file bibfile)
2387 (delete-file texfile)
2388 (delete-file tempname)
2390 ;; Now back to the original org buffer and insert the results
2391 (switch-to-buffer cb)
2392 (when (not (string= "" results))
2394 (goto-char (point-max))
2396 (org-insert-heading)
2397 (insert (format " Bibtex entries
2399 ,#+BEGIN_SRC text :tangle %s
2401 ,#+END_SRC" (concat (file-name-sans-extension (file-name-nondirectory (buffer-file-name))) ".bib") results))))))
2404 ** Find bad cite links
2405 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.
2407 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2410 (defun index (substring list)
2411 "return the index of string in a list of strings"
2414 (dolist (arg list i)
2415 (if (string-match (concat "^" substring "$") arg)
2420 ;; return counter if found, otherwise return nil
2424 (defun org-ref-find-bad-citations ()
2425 "Create a list of citation keys in an org-file that do not have a bibtex entry in the known bibtex files.
2427 Makes a new buffer with clickable links."
2429 ;; generate the list of bibtex-keys and cited keys
2430 (let* ((bibtex-files (org-ref-find-bibliography))
2431 (bibtex-file-path (mapconcat (lambda (x) (file-name-directory (file-truename x))) bibtex-files ":"))
2432 (bibtex-keys (mapcar (lambda (x) (car x)) (bibtex-global-key-alist)))
2433 (bad-citations '()))
2435 (org-element-map (org-element-parse-buffer) 'link
2437 (let ((plist (nth 1 link)))
2438 (when (equal (plist-get plist ':type) "cite")
2439 (dolist (key (org-ref-split-and-strip-string (plist-get plist ':path)) )
2440 (when (not (index key bibtex-keys))
2441 (setq bad-citations (append bad-citations
2442 `(,(format "%s [[elisp:(progn (switch-to-buffer-other-frame \"%s\")(goto-char %s))][not found here]]\n"
2443 key (buffer-name)(plist-get plist ':begin)))))
2448 (switch-to-buffer-other-window "*Missing citations*")
2451 (insert "* List of bad cite links\n")
2452 (insert (mapconcat 'identity bad-citations ""))
2453 ;(setq buffer-read-only t)
2454 (use-local-map (copy-keymap org-mode-map))
2455 (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))
2457 (when (get-buffer "*Missing citations*")
2458 (kill-buffer "*Missing citations*"))
2459 (message "No bad cite links found"))))
2462 ** Finding non-ascii characters
2463 I like my bibtex files to be 100% ascii. This function finds the non-ascii characters so you can replace them.
2465 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2466 (defun org-ref-find-non-ascii-characters ()
2467 "finds non-ascii characters in the buffer. Useful for cleaning up bibtex files"
2469 (occur "[^[:ascii:]]"))
2472 ** Resort a bibtex entry
2473 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.
2475 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2476 (defun org-ref-sort-bibtex-entry ()
2477 "sort fields of entry in standard order and downcase them"
2479 (bibtex-beginning-of-entry)
2480 (let* ((master '("author" "title" "journal" "volume" "number" "pages" "year" "doi" "url"))
2481 (entry (bibtex-parse-entry))
2484 (type (cdr (assoc "=type=" entry)))
2485 (key (cdr (assoc "=key=" entry))))
2487 ;; these are the fields we want to order that are in this entry
2488 (setq entry-fields (mapcar (lambda (x) (car x)) entry))
2489 ;; we do not want to reenter these fields
2490 (setq entry-fields (remove "=key=" entry-fields))
2491 (setq entry-fields (remove "=type=" entry-fields))
2493 ;;these are the other fields in the entry
2494 (setq other-fields (remove-if-not (lambda(x) (not (member x master))) entry-fields))
2497 ;; right now we only resort articles
2498 ((string= (downcase type) "article")
2501 (concat "@article{" key ",\n"
2504 (when (member field entry-fields)
2505 (format "%s = %s," (downcase field) (cdr (assoc field entry))))) master "\n")
2508 (format "%s = %s," (downcase field) (cdr (assoc field entry)))) other-fields "\n")
2510 (bibtex-find-entry key)
2512 (bibtex-clean-entry)
2516 ** Clean a bibtex entry
2517 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.
2518 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.
2519 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2520 (defun org-ref-clean-bibtex-entry(&optional keep-key)
2521 "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"
2523 (bibtex-beginning-of-entry)
2525 ;; some entries do not have a key or comma in first line. We check and add it, if needed.
2526 (unless (string-match ",$" (thing-at-point 'line))
2530 ;; check for empty pages, and put eid or article id in its place
2531 (let ((entry (bibtex-parse-entry))
2532 (pages (bibtex-autokey-get-field "pages"))
2533 (year (bibtex-autokey-get-field "year"))
2534 (doi (bibtex-autokey-get-field "doi"))
2535 ;; The Journal of Chemical Physics uses eid
2536 (eid (bibtex-autokey-get-field "eid")))
2538 ;; replace http://dx.doi.org/ in doi. some journals put that in,
2539 ;; but we only want the doi.
2540 (when (string-match "^http://dx.doi.org/" doi)
2541 (bibtex-beginning-of-entry)
2542 (goto-char (car (cdr (bibtex-search-forward-field "doi" t))))
2544 (bibtex-make-field "doi")
2546 (insert (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))
2548 ;; asap articles often set year to 0, which messes up key
2549 ;; generation. fix that.
2550 (when (string= "0" year)
2551 (bibtex-beginning-of-entry)
2552 (goto-char (car (cdr (bibtex-search-forward-field "year" t))))
2554 (bibtex-make-field "year")
2556 (insert (read-string "Enter year: ")))
2558 ;; fix pages if they are empty if there is an eid to put there.
2559 (when (string= "-" pages)
2561 (bibtex-beginning-of-entry)
2562 ;; this seems like a clunky way to set the pages field.But I
2563 ;; cannot find a better way.
2564 (goto-char (car (cdr (bibtex-search-forward-field "pages" t))))
2566 (bibtex-make-field "pages")
2570 ;; replace naked & with \&
2572 (bibtex-narrow-to-entry)
2573 (bibtex-beginning-of-entry)
2574 (message "checking &")
2575 (replace-regexp " & " " \\\\& ")
2578 ;; generate a key, and if it duplicates an existing key, edit it.
2580 (let ((key (bibtex-generate-autokey)))
2582 ;; first we delete the existing key
2583 (bibtex-beginning-of-entry)
2584 (re-search-forward bibtex-entry-maybe-empty-head)
2585 (if (match-beginning bibtex-key-in-head)
2586 (delete-region (match-beginning bibtex-key-in-head)
2587 (match-end bibtex-key-in-head)))
2588 ;; check if the key is in the buffer
2589 (when (save-excursion
2590 (bibtex-search-entry key))
2592 (bibtex-search-entry key)
2593 (bibtex-copy-entry-as-kill)
2594 (switch-to-buffer-other-window "*duplicate entry*")
2596 (setq key (bibtex-read-key "Duplicate Key found, edit: " key)))
2599 (kill-new key))) ;; save key for pasting
2601 ;; run hooks. each of these operates on the entry with no arguments.
2602 ;; this did not work like i thought, it gives a symbolp error.
2603 ;; (run-hooks org-ref-clean-bibtex-entry-hook)
2608 org-ref-clean-bibtex-entry-hook)
2610 ;; sort fields within entry
2611 (org-ref-sort-bibtex-entry)
2612 ;; check for non-ascii characters
2613 (occur "[^[:ascii:]]")
2618 : org-ref-clean-bibtex-entry
2620 ** Sort the entries in a citation link by year
2621 I prefer citations in chronological order within a grouping. These functions sort the link under the cursor by year.
2623 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2624 (defun org-ref-get-citation-year (key)
2625 "get the year of an entry with key. Returns year as a string."
2627 (let* ((results (org-ref-get-bibtex-key-and-file key))
2628 (bibfile (cdr results)))
2630 (insert-file-contents bibfile)
2631 (bibtex-search-entry key nil 0)
2632 (prog1 (reftex-get-bib-field "year" (bibtex-parse-entry t))
2635 (defun org-ref-sort-citation-link ()
2636 "replace link at point with sorted link by year"
2638 (let* ((object (org-element-context))
2639 (type (org-element-property :type object))
2640 (begin (org-element-property :begin object))
2641 (end (org-element-property :end object))
2642 (link-string (org-element-property :path object))
2644 (setq keys (org-ref-split-and-strip-string link-string))
2645 (setq years (mapcar 'org-ref-get-citation-year keys))
2646 (setq data (mapcar* (lambda (a b) `(,a . ,b)) years keys))
2647 (setq data (cl-sort data (lambda (x y) (< (string-to-int (car x)) (string-to-int (car y))))))
2648 ;; now get the keys separated by commas
2649 (setq keys (mapconcat (lambda (x) (cdr x)) data ","))
2650 ;; and replace the link with the sorted keys
2651 (cl--set-buffer-substring begin end (concat type ":" keys))))
2654 ** Sort entries in citation links with shift-arrow keys
2655 Sometimes it may be helpful to manually change the order of citations. These functions define shift-arrow functions.
2656 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2657 (defun org-ref-swap-keys (i j keys)
2658 "swap the keys in a list with index i and j"
2659 (let ((tempi (nth i keys)))
2660 (setf (nth i keys) (nth j keys))
2661 (setf (nth j keys) tempi))
2664 (defun org-ref-swap-citation-link (direction)
2665 "move citation at point in direction +1 is to the right, -1 to the left"
2667 (let* ((object (org-element-context))
2668 (type (org-element-property :type object))
2669 (begin (org-element-property :begin object))
2670 (end (org-element-property :end object))
2671 (link-string (org-element-property :path object))
2673 ;; We only want this to work on citation links
2674 (when (-contains? org-ref-cite-types type)
2675 (setq key (org-ref-get-bibtex-key-under-cursor))
2676 (setq keys (org-ref-split-and-strip-string link-string))
2677 (setq i (index key keys)) ;; defined in org-ref
2678 (if (> direction 0) ;; shift right
2679 (org-ref-swap-keys i (+ i 1) keys)
2680 (org-ref-swap-keys i (- i 1) keys))
2681 (setq keys (mapconcat 'identity keys ","))
2682 ;; and replace the link with the sorted keys
2683 (cl--set-buffer-substring begin end (concat type ":" keys " "))
2684 ;; now go forward to key so we can move with the key
2685 (re-search-forward key)
2686 (goto-char (match-beginning 0)))))
2688 ;; add hooks to make it work
2689 (add-hook 'org-shiftright-hook (lambda () (org-ref-swap-citation-link 1)))
2690 (add-hook 'org-shiftleft-hook (lambda () (org-ref-swap-citation-link -1)))
2693 I like convenience. Here are some aliases for faster typing.
2695 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2696 (defalias 'oro 'org-ref-open-citation-at-point)
2697 (defalias 'orc 'org-ref-citation-at-point)
2698 (defalias 'orp 'org-ref-open-pdf-at-point)
2699 (defalias 'oru 'org-ref-open-url-at-point)
2700 (defalias 'orn 'org-ref-open-notes-at-point)
2701 (defalias 'ornr 'org-ref-open-notes-from-reftex)
2703 (defalias 'orib 'org-ref-insert-bibliography-link)
2704 (defalias 'oric 'org-ref-insert-cite-link)
2705 (defalias 'orir 'org-ref-insert-ref-link)
2706 (defalias 'orsl 'org-ref-store-bibtex-entry-link)
2708 (defalias 'orcb 'org-ref-clean-bibtex-entry)
2711 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
2716 This code will tangle the elisp code out to org-ref.el and load it.
2718 [[elisp:(progn (org-babel-tangle) (load-file "org-ref.el"))]]
2720 Alternatively you may use:
2722 [[elisp:(org-babel-load-file "org-ref.org")]]