1 ;;; org-ref.el --- cite and cross-reference in org-mode
3 ;; Copyright(C) 2014 John Kitchin
5 ;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
6 ;; URL: https://github.com/jkitchin/org-ref
8 ;; Keywords: org-mode, cite, ref, label
9 ;; Package-Requires: ((org) (dash) (helm) (helm-bibtex) (hydra))
11 ;; This file is not currently part of GNU Emacs.
13 ;; This program is free software; you can redistribute it and/or
14 ;; modify it under the terms of the GNU General Public License as
15 ;; published by the Free Software Foundation; either version 2, or (at
16 ;; your option) any later version.
18 ;; This program is distributed in the hope that it will be useful, but
19 ;; WITHOUT ANY WARRANTY; without even the implied warranty of
20 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
21 ;; General Public License for more details.
23 ;; You should have received a copy of the GNU General Public License
24 ;; along with this program ; see the file COPYING. If not, write to
25 ;; the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
26 ;; Boston, MA 02111-1307, USA.
30 ;; Lisp code to setup bibliography cite, ref and label org-mode links.
31 ;; also sets up reftex and helm for org-mode citations. The links are
32 ;; clickable and do things that are useful. You should really read
33 ;; org-ref.org for details.
38 (require 'reftex-cite)
41 (require 'helm-config)
42 (require 'helm-bibtex)
47 "Customization group for org-ref.")
49 (defcustom org-ref-bibliography-notes
51 "Filename where you will put all your notes about an entry in the default bibliography."
55 (defcustom org-ref-default-bibliography
57 "List of bibtex files to search for.
58 You should use full-paths for each file."
59 :type '(repeat :tag "List of bibtex files" file)
62 (defcustom org-ref-pdf-directory
64 "Directory where pdfs are stored by key. put a trailing / in."
68 (defcustom org-ref-default-citation-link
70 "The default type of citation link to use."
74 (defcustom org-ref-insert-cite-key
76 "Keyboard shortcut to insert a citation."
80 (defcustom org-ref-bibliography-entry-format
81 '(("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>.")
83 ("book" . "%a, %t, %u (%y).")
85 ("proceedings" . "%e, %t in %S, %u (%y).")
87 ("inproceedings" . "%a, %t, %p, in %b, edited by %e, %u (%y)"))
89 "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."
93 (defcustom org-ref-open-notes-function
99 ;;(org-tree-to-indirect-buffer)
100 (outline-previous-visible-heading 1)
101 (recenter-top-bottom 0))
102 "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."
107 (defcustom org-ref-open-pdf-function
108 'org-ref-open-pdf-at-point
109 "User-defined function to open a pdf from a link. The function must get the key at point, and derive a path to the pdf file, then open it. The default function is `org-ref-open-pdf-at-point'."
114 (defcustom org-ref-insert-cite-function
115 'org-ref-helm-insert-cite-link
116 "Function to call to insert citation links. The default is `org-ref-helm-insert-cite-link' which uses `helm-bibtex'. `org-ref' modifies `helm-bibtex' a little bit to give `org-mode' citations, and to reorder default actions. You may use `org-ref-insert-cite-link' if you like the reftex interface."
121 (defcustom org-ref-cite-onclick-function
122 'org-ref-cite-click-helm
123 "Function that runs when you click on a cite link. The function must take no arguments. You may also use `org-ref-cite-onclick-minibuffer-menu' if you do not like helm. If you like `hydra', consider using `org-ref-cite-hydra'."
128 (defcustom org-ref-show-citation-on-enter t
129 "If non-nil add a hook function to show the citation summary in the minibuffer."
132 (defcustom org-ref-cite-types
133 '("cite" "nocite" ;; the default latex cite commands
134 ;; natbib cite commands, http://ctan.unixbrain.com/macros/latex/contrib/natbib/natnotes.pdf
135 "citet" "citet*" "citep" "citep*"
136 "citealt" "citealt*" "citealp" "citealp*"
138 "citeauthor" "citeauthor*"
139 "citeyear" "citeyear*"
140 "Citet" "Citep" "Citealt" "Citealp" "Citeauthor"
142 ;; http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf
144 "parencite" "Parencite"
145 "footcite" "footcitetext"
146 "textcite" "Textcite"
147 "smartcite" "Smartcite"
148 "cite*" "parencite*" "supercite"
149 "autocite" "Autocite" "autocite*" "Autocite*"
151 "citetitle" "citetitle*"
152 "citedate" "citedate*"
154 "fullcite" "footfullcite"
155 ;; "volcite" "Volcite" cannot support the syntax
156 "notecite" "Notecite"
157 "pnotecite" "Pnotecite"
159 ;; multicites. Very limited support for these.
160 "cites" "Cites" "parencites" "Parencites"
161 "footcites" "footcitetexts"
162 "smartcites" "Smartcites" "textcites" "Textcites"
163 "supercites" "autocites" "Autocites"
164 ;; for the bibentry package
167 "List of citation types known in `org-ref'."
168 :type '(repeat :tag "List of citation types" string)
171 (defcustom org-ref-clean-bibtex-entry-hook nil
172 "Hook that is run in `org-ref-clean-bibtex-entry'. The functions should take no arguments, and operate on the bibtex entry at point."
176 (defvar org-ref-bibliography-files
178 "Variable to hold bibliography files to be searched.")
180 ;; * org-mode / reftex setup
182 (defun org-mode-reftex-setup ()
183 "Setup `org-mode' and reftex for org-ref."
184 (and (buffer-file-name)
185 (file-exists-p (buffer-file-name))
186 (global-auto-revert-mode t))
187 (make-local-variable 'reftex-cite-format)
188 (setq reftex-cite-format 'org))
190 ;; define key for inserting citations
191 (define-key org-mode-map
192 (kbd org-ref-insert-cite-key)
193 org-ref-insert-cite-function)
195 (add-hook 'org-mode-hook 'org-mode-reftex-setup)
197 (eval-after-load 'reftex-vars
199 (add-to-list 'reftex-cite-format-builtin
200 '(org "Org-mode citation"
201 ((?\C-m . "cite:%l") ; default
202 (?d . ",%l") ; for appending
208 (?h . "citeauthor:%l")
209 (?H . "citeauthor*:%l")
215 ;; * Messages for link at cursor
216 (defvar org-ref-message-timer nil
217 "Variable to store the link message timer in.")
220 (defun org-ref-show-link-messages ()
221 "Turn on link messages.
222 You will see a message in the minibuffer when on a cite, ref or label link."
224 (or org-ref-message-timer
225 (setq org-ref-message-timer
226 (run-with-idle-timer 0.5 t 'org-ref-link-message))))
229 (defun org-ref-cancel-link-messages ()
230 "Stop showing messages in minibuffer when on a link."
232 (cancel-timer org-ref-message-timer)
233 (setq org-ref-message-timer nil))
236 (when org-ref-show-citation-on-enter
237 (org-ref-show-link-messages))
239 ;; ** Messages for context under mouse pointer
241 (defvar org-ref-last-mouse-pos nil
242 "Stores last mouse position for use in `org-ref-mouse-message'.")
244 (defun org-ref-can-move-p ()
245 "See if a character is under the mouse. If so return the position for `goto-char'."
246 (let* ((line (cddr org-ref-last-mouse-pos))
247 (col (cadr org-ref-last-mouse-pos)))
249 (goto-char (window-start))
252 (> (- (line-end-position) (line-beginning-position)) col)
253 (progn (forward-char col) (point))
257 (defun org-ref-mouse-message ()
258 "Display message for link under mouse cursor."
260 (when (not (equal (mouse-position) org-ref-last-mouse-pos))
261 (setq org-ref-last-mouse-pos (mouse-position))
262 (let ((p (org-ref-can-move-p)))
266 (org-ref-link-message))))))
269 (defvar org-ref-message-timer-mouse nil
270 "Store mouse timer.")
273 (defvar org-ref-mouse-message-interval 0.5
274 "How often to run the mouse message timer in seconds.")
277 (defun org-ref-mouse-messages-on ()
278 "Turn on mouse messages."
280 (or org-ref-message-timer-mouse
281 (setq org-ref-message-timer-mouse
282 (run-at-time "0.5 sec"
283 org-ref-mouse-message-interval
284 'org-ref-mouse-message))))
287 (defun org-ref-mouse-messages-off ()
288 "Turn off mouse messages."
290 (cancel-timer org-ref-message-timer-mouse)
291 (setq org-ref-message-timer-mouse nil)
292 (message "Mouse messages are off"))
294 ;; Colorizing org-ref links
295 (defcustom org-ref-colorize-links
297 "When non-nil, change colors of links."
301 (defcustom org-ref-cite-color
303 "Color of cite like links."
307 (defcustom org-ref-ref-color
309 "Color of ref like links."
313 (defcustom org-ref-label-color
315 "Color of label links."
319 (defvar org-ref-cite-re nil
320 "Regexp for cite links.")
323 (setq org-ref-cite-re
324 (concat "\\(" (mapconcat
326 (replace-regexp-in-string "\*" "\\\\*" x)
328 org-ref-cite-types "\\|") "\\)"
329 ":\\([a-zA-Z0-9-_:\\./]*,?\\)*"))
332 (setq org-ref-label-re
333 "label:\\([a-zA-Z0-9-_:]*,?\\)*")
337 "\\(eq\\)?ref:\\([a-zA-Z0-9-_:]*,?\\)*")
340 (defface org-ref-cite-face
341 `((t (:inherit org-link :foreground ,org-ref-cite-color)))
342 "Color for cite-like links in org-ref.")
345 (defface org-ref-label-face
346 `((t (:inherit org-link :foreground ,org-ref-label-color)))
347 "Color for ref links in org-ref.")
350 (defface org-ref-ref-face
351 `((t (:inherit org-link :foreground ,org-ref-ref-color)))
352 "Face for ref links in org-ref.")
355 (defun org-ref-colorize-links ()
356 "Colorize org-ref links."
358 (highlight-regexp org-ref-cite-re 'org-ref-cite-face)
359 (highlight-regexp org-ref-label-re 'org-ref-label-face)
360 (highlight-regexp org-ref-ref-re 'org-ref-ref-face))
363 (when org-ref-colorize-links
364 (add-hook 'org-mode-hook 'org-ref-colorize-links))
366 ;; * General org-ref utilities
367 (defun org-ref-strip-string (string)
368 "Strip leading and trailing whitespace from the STRING."
369 (replace-regexp-in-string
370 (concat search-whitespace-regexp "$" ) ""
371 (replace-regexp-in-string
372 (concat "^" search-whitespace-regexp ) "" string)))
374 (defun org-ref-split-and-strip-string (string)
375 "Split key-string and strip keys in STRING.
376 Assumes the key-string is comma delimited."
377 (mapcar 'org-ref-strip-string (split-string string ",")))
379 (defun org-ref-reftex-get-bib-field (field entry &optional format)
380 "Similar to reftex-get-bib-field, but removes enclosing braces and quotes in FIELD in the bibtex ENTRY.
381 Optional argument FORMAT bibtex format."
383 (setq result (reftex-get-bib-field field entry format))
384 (when (and (not (string= result "")) (string= "{" (substring result 0 1)))
385 (setq result (substring result 1 -1)))
386 (when (and (not (string= result "")) (string= "\"" (substring result 0 1)))
387 (setq result (substring result 1 -1)))
390 (defun org-ref-reftex-format-citation (entry format)
391 "Return a formatted string for the bibtex ENTRY (from bibtex-parse-entry) according to the FORMAT argument.
392 The format is a string with these percent escapes.
394 In the format, the following percent escapes will be expanded.
396 %l The BibTeX label of the citation.
397 %a List of author names, see also `reftex-cite-punctuation'.
398 %2a Like %a, but abbreviate more than 2 authors like Jones et al.
399 %A First author name only.
400 %e Works like %a, but on list of editor names. (%2e and %E work a well)
402 It is also possible to access all other BibTeX database fields:
403 %b booktitle %c chapter %d edition %h howpublished
404 %i institution %j journal %k key %m month
405 %n number %o organization %p pages %P first page
406 %r address %s school %u publisher %t title
408 %B booktitle, abbreviated %T title, abbreviated
413 Usually, only %l is needed. The other stuff is mainly for the echo area
414 display, and for (setq reftex-comment-citations t).
416 %< as a special operator kills punctuation and space around it after the
417 string has been formatted.
419 A pair of square brackets indicates an optional argument, and RefTeX
420 will prompt for the values of these arguments.
422 Beware that all this only works with BibTeX database files. When
423 citations are made from the \bibitems in an explicit thebibliography
424 environment, only %l is available."
425 ;; Format a citation from the info in the BibTeX ENTRY
426 (unless (stringp format) (setq format "\\cite{%l}"))
428 (if (and reftex-comment-citations
429 (string-match "%l" reftex-cite-comment-format))
430 (error "Reftex-cite-comment-format contains invalid %%l"))
433 "\\(\\`\\|[^%]\\)\\(\\(%\\([0-9]*\\)\\([a-zA-Z]\\)\\)[.,;: ]*\\)"
435 (let ((n (string-to-number (match-string 4 format)))
436 (l (string-to-char (match-string 5 format)))
442 (org-ref-reftex-get-bib-field "&key" entry)
443 (if reftex-comment-citations
444 reftex-cite-comment-format
446 ((= l ?a) (reftex-format-names
447 (reftex-get-bib-names "author" entry)
449 ((= l ?A) (car (reftex-get-bib-names "author" entry)))
450 ((= l ?b) (org-ref-reftex-get-bib-field "booktitle" entry "in: %s"))
451 ((= l ?B) (reftex-abbreviate-title
452 (org-ref-reftex-get-bib-field "booktitle" entry "in: %s")))
453 ((= l ?c) (org-ref-reftex-get-bib-field "chapter" entry))
454 ((= l ?d) (org-ref-reftex-get-bib-field "edition" entry))
455 ((= l ?D) (org-ref-reftex-get-bib-field "doi" entry))
456 ((= l ?e) (reftex-format-names
457 (reftex-get-bib-names "editor" entry)
459 ((= l ?E) (car (reftex-get-bib-names "editor" entry)))
460 ((= l ?h) (org-ref-reftex-get-bib-field "howpublished" entry))
461 ((= l ?i) (org-ref-reftex-get-bib-field "institution" entry))
462 ((= l ?j) (org-ref-reftex-get-bib-field "journal" entry))
463 ((= l ?k) (org-ref-reftex-get-bib-field "key" entry))
464 ((= l ?m) (org-ref-reftex-get-bib-field "month" entry))
465 ((= l ?n) (org-ref-reftex-get-bib-field "number" entry))
466 ((= l ?o) (org-ref-reftex-get-bib-field "organization" entry))
467 ((= l ?p) (org-ref-reftex-get-bib-field "pages" entry))
468 ((= l ?P) (car (split-string
469 (org-ref-reftex-get-bib-field "pages" entry)
471 ((= l ?s) (org-ref-reftex-get-bib-field "school" entry))
472 ((= l ?S) (org-ref-reftex-get-bib-field "series" entry))
473 ((= l ?u) (org-ref-reftex-get-bib-field "publisher" entry))
474 ((= l ?U) (org-ref-reftex-get-bib-field "url" entry))
475 ((= l ?r) (org-ref-reftex-get-bib-field "address" entry))
476 ;; strip enclosing brackets from title if they are there
477 ((= l ?t) (org-ref-reftex-get-bib-field "title" entry))
478 ((= l ?T) (reftex-abbreviate-title
479 (org-ref-reftex-get-bib-field "title" entry)))
480 ((= l ?v) (org-ref-reftex-get-bib-field "volume" entry))
481 ((= l ?y) (org-ref-reftex-get-bib-field "year" entry)))))
484 (setq b (match-beginning 2) e (match-end 2))
485 (setq b (match-beginning 3) e (match-end 3)))
486 (setq format (concat (substring format 0 b) rpl (substring format e)))))
487 (while (string-match "%%" format)
488 (setq format (replace-match "%" t t format)))
489 (while (string-match "[ ,.;:]*%<" format)
490 (setq format (replace-match "" t t format)))
491 ;; also replace carriage returns, tabs, and multiple whitespaces
492 (setq format (replace-regexp-in-string "\n\\|\t\\|\s+" " " format))
495 (defun org-ref-get-bibtex-entry-citation (key)
496 "Return a string for the bibliography entry corresponding to KEY.
497 Format according to the type in `org-ref-bibliography-entry-format'."
499 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
500 (file) (entry) (bibtex-entry) (entry-type) (format))
502 (setq file (catch 'result
503 (loop for file in org-ref-bibliography-files do
504 (if (org-ref-key-in-file-p key (file-truename file))
506 (message "%s not found in %s"
507 key (file-truename file))))))
510 (insert-file-contents file)
511 (bibtex-search-entry key nil 0)
512 (setq bibtex-entry (bibtex-parse-entry))
513 (setq entry-type (downcase (cdr (assoc "=type=" bibtex-entry))))
514 (setq format (cdr (assoc entry-type org-ref-bibliography-entry-format)))
516 (setq entry (org-ref-reftex-format-citation bibtex-entry format))
518 (bibtex-narrow-to-entry)
519 (setq entry (buffer-string)))))
522 (defun org-ref-get-bibtex-keys ()
523 "Return a list of unique keys in the buffer."
525 (org-element-map (org-element-parse-buffer) 'link
527 (let ((plist (nth 1 link)))
528 (when (-contains? org-ref-cite-types (plist-get plist ':type))
531 (org-ref-split-and-strip-string (plist-get plist ':path)))
532 (when (not (-contains? keys key))
533 (setq keys (append keys (list key))))))))
534 ;; set with-affiliated to get keys in captions
536 ;; Sort keys alphabetically
537 (setq keys (cl-sort keys 'string-lessp :key 'downcase))
540 (defun org-ref-get-bibtex-entry-html (key)
541 "Return an html string for the bibliography entry corresponding to KEY."
542 (format "<li><a id=\"%s\">[%s] %s</a></li>"
543 key key (org-ref-get-bibtex-entry-citation key)))
545 (defun org-ref-get-html-bibliography ()
546 "Create an html bibliography when there are keys."
547 (let ((keys (org-ref-get-bibtex-keys)))
549 (concat "<h1>Bibliography</h1>
551 (mapconcat (lambda (x) (org-ref-get-bibtex-entry-html x)) keys "\n")
554 (defun org-ref-get-bibtex-entry-org (key)
555 "Return an org string for the bibliography entry corresponding to KEY."
556 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
557 (file) (entry) (bibtex-entry) (entry-type) (format))
559 (setq file (catch 'result
560 (loop for file in org-ref-bibliography-files do
561 (if (org-ref-key-in-file-p key (file-truename file))
563 (message "%s not found in %s" key (file-truename file))))))
566 (insert-file-contents file)
567 (bibtex-search-entry key nil 0)
568 (setq entry (bibtex-parse-entry))
573 " (org-ref-reftex-get-bib-field "author" entry)
574 (org-ref-reftex-get-bib-field "title" entry)
575 (concat " :CUSTOM_ID: " (org-ref-reftex-get-bib-field "=key=" entry) "\n"
576 (mapconcat (lambda (element) (format " :%s: %s"
577 (upcase (car element))
582 (defun org-ref-get-org-bibliography ()
583 "Create an org bibliography when there are keys."
584 (let ((keys (org-ref-get-bibtex-keys)))
586 (concat "* Bibliography
588 (mapconcat (lambda (x) (org-ref-get-bibtex-entry-org x)) keys "\n")
591 (defun org-ref-get-bibtex-entry-ascii (key)
592 "Return an ascii string for the bibliography entry corresponding to KEY."
594 (format "[%s] %s" key (org-ref-get-bibtex-entry-citation key)))
596 (defun org-ref-get-ascii-bibliography ()
597 "Create an html bibliography when there are keys."
598 (let ((keys (org-ref-get-bibtex-keys)))
604 (mapconcat (lambda (x) (org-ref-get-bibtex-entry-ascii x)) keys "\n")
608 ;; ** bibliography and bibliographystyle
609 (org-add-link-type "bibliography"
610 ;; this code is run on clicking. The bibliography
611 ;; may contain multiple files. this code finds the
612 ;; one you clicked on and opens it.
613 (lambda (link-string)
614 ;; get link-string boundaries we have to go to the
615 ;; beginning of the line, and then search forward
617 ;; object is the link you clicked on
618 (object (org-element-context))
619 (link-string-beginning)
623 (goto-char (org-element-property :begin object))
624 (search-forward link-string nil nil 1)
625 (setq link-string-beginning (match-beginning 0))
626 (setq link-string-end (match-end 0)))
628 ;; Make sure point is in the link-path.
629 (if (< cp link-string-beginning)
630 (goto-char link-string-beginning))
631 ;; We set the reftex-default-bibliography
632 ;; here. it should be a local variable only in
633 ;; the current buffer. We need this for using
634 ;; reftex to do citations.
635 (set (make-local-variable 'reftex-default-bibliography)
637 (org-element-property :path object) ","))
639 ;; now if we have comma separated bibliographies
640 ;; we find the one clicked on. we want to
641 ;; search forward to next comma from point
643 (if (search-forward "," link-string-end 1 1)
645 (setq key-end (- (match-end 0) 1))
646 ;; no comma found so take the point
647 (setq key-end (point))))
648 ;; and backward to previous comma from point
650 (if (search-backward "," link-string-beginning 1 1)
652 (setq key-beginning (+ (match-beginning 0) 1))
653 (setq key-beginning (point)))) ; no match found
654 ;; save the key we clicked on.
655 (setq bibfile (org-ref-strip-string
656 (buffer-substring key-beginning key-end)))
657 ;; open file on click
658 (find-file bibfile)))
661 (lambda (keyword desc format)
663 ((eq format 'org) (org-ref-get-org-bibliography))
664 ((eq format 'ascii) (org-ref-get-ascii-bibliography))
665 ((eq format 'html) (org-ref-get-html-bibliography))
667 ;; write out the latex bibliography command
668 (format "\\bibliography{%s}"
669 (replace-regexp-in-string
673 (mapcar 'expand-file-name
674 (split-string keyword ","))
677 (org-add-link-type "nobibliography"
678 ;; this code is run on clicking. The bibliography
679 ;; may contain multiple files. this code finds the
680 ;; one you clicked on and opens it.
681 (lambda (link-string)
682 ;; get link-string boundaries
683 ;; we have to go to the beginning of the line, and then search forward
686 ;; object is the link you clicked on
687 (object (org-element-context))
689 (link-string-beginning)
693 (goto-char (org-element-property :begin object))
694 (search-forward link-string nil nil 1)
695 (setq link-string-beginning (match-beginning 0))
696 (setq link-string-end (match-end 0)))
698 ;; We set the reftex-default-bibliography
699 ;; here. it should be a local variable only in
700 ;; the current buffer. We need this for using
701 ;; reftex to do citations.
702 (set (make-local-variable 'reftex-default-bibliography)
703 (split-string (org-element-property :path object) ","))
705 ;; now if we have comma separated bibliographies
706 ;; we find the one clicked on. we want to
707 ;; search forward to next comma from point
709 (if (search-forward "," link-string-end 1 1)
710 (setq key-end (- (match-end 0) 1)) ; we found a match
711 (setq key-end (point)))) ; no comma found so take the point
712 ;; and backward to previous comma from point
714 (if (search-backward "," link-string-beginning 1 1)
715 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
716 (setq key-beginning (point)))) ; no match found
717 ;; save the key we clicked on.
718 (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
719 (find-file bibfile))) ; open file on click
722 (lambda (keyword desc format)
724 ((eq format 'org) (org-ref-get-org-bibliography))
725 ((eq format 'ascii) (org-ref-get-ascii-bibliography))
726 ((eq format 'html) (org-ref-get-html-bibliography))
728 ;; write out the latex bibliography command
729 (format "\\nobibliography{%s}"
730 (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
731 (mapcar 'expand-file-name
732 (split-string keyword ","))
735 (org-add-link-type "printbibliography"
736 (lambda (arg) (message "Nothing implemented for clicking here."))
737 (lambda (keyword desc format)
739 ((eq format 'org) (org-ref-get-org-bibliography))
740 ((eq format 'html) (org-ref-get-html-bibliography))
742 ;; write out the biblatex bibliography command
743 "\\printbibliography"))))
745 (org-add-link-type "bibliographystyle"
746 (lambda (arg) (message "Nothing implemented for clicking here."))
747 (lambda (keyword desc format)
750 ;; write out the latex bibliography command
751 (format "\\bibliographystyle{%s}" keyword))
752 ;; Other styles should not have an output for this
757 (defun org-bibliographystyle-complete-link (&optional arg)
758 "Completion function for bibliographystyle link.
760 (format "bibliographystyle:%s" (ido-completing-read
762 '("unsrt" "plain" "alpha"
764 ;; https://www.sharelatex.com/learn/Natbib_bibliography_styles
765 "dinat" "humannat" "plainnat"
766 "abbrnat" "unsrtnat" "rusnat"
770 (defun org-bibliography-complete-link (&optional arg)
771 "Completion function for bibliography link.
773 (format "bibliography:%s" (read-file-name "enter file: " nil nil t)))
776 (defun org-ref-insert-bibliography-link ()
777 "Insert a bibliography with completion."
779 (insert (org-bibliography-complete-link)))
783 (org-add-link-type "addbibresource"
784 ;; this code is run on clicking. The addbibresource
785 ;; may contain multiple files. this code finds the
786 ;; one you clicked on and opens it.
787 (lambda (link-string)
788 ;; get link-string boundaries
789 ;; we have to go to the beginning of the line, and then search forward
792 ;; object is the link you clicked on
793 (object (org-element-context))
795 (link-string-beginning)
799 (goto-char (org-element-property :begin object))
800 (search-forward link-string nil nil 1)
801 (setq link-string-beginning (match-beginning 0))
802 (setq link-string-end (match-end 0)))
804 ;; We set the reftex-default-addbibresource
805 ;; here. it should be a local variable only in
806 ;; the current buffer. We need this for using
807 ;; reftex to do citations.
808 (set (make-local-variable 'reftex-default-addbibresource)
809 (split-string (org-element-property :path object) ","))
811 ;; now if we have comma separated bibliographies
812 ;; we find the one clicked on. we want to
813 ;; search forward to next comma from point
815 (if (search-forward "," link-string-end 1 1)
816 (setq key-end (- (match-end 0) 1)) ; we found a match
817 (setq key-end (point)))) ; no comma found so take the point
818 ;; and backward to previous comma from point
820 (if (search-backward "," link-string-beginning 1 1)
821 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
822 (setq key-beginning (point)))) ; no match found
823 ;; save the key we clicked on.
824 (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
825 (find-file bibfile))) ; open file on click
828 (lambda (keyword desc format)
830 ((eq format 'html) (format "")); no output for html
832 ;; write out the latex addbibresource command
833 (format "\\addbibresource{%s}" keyword)))))
835 ;; ** List of figures
836 (defun org-ref-list-of-figures (&optional arg)
837 "Generate buffer with list of figures in them.
840 (save-excursion (widen)
841 (let* ((c-b (buffer-name))
844 (org-element-map (org-element-parse-buffer) 'link
846 "create a link for to the figure"
848 (and (string= (org-element-property :type link) "file")
850 "[^.]*\\.\\(png\\|jpg\\|eps\\|pdf\\)$"
851 (org-element-property :path link)))
854 (let* ((start (org-element-property :begin link))
855 (parent (car (cdr (org-element-property :parent link))))
856 (caption (caaar (plist-get parent :caption)))
857 (name (plist-get parent :name)))
860 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]] %s\n"
861 c-b start counter (or name "") caption)
863 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]]\n"
864 c-b start counter (or name "")))))))))
865 (switch-to-buffer "*List of Figures*")
866 (setq buffer-read-only nil)
869 (insert (mapconcat 'identity list-of-figures ""))
870 (setq buffer-read-only t)
871 (use-local-map (copy-keymap org-mode-map))
872 (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
876 'org-ref-list-of-figures ; on click
877 (lambda (keyword desc format)
880 (format "\\listoffigures")))))
883 (defun org-ref-list-of-tables (&optional arg)
884 "Generate a buffer with a list of tables.
889 (let* ((c-b (buffer-name))
892 (org-element-map (org-element-parse-buffer 'element) 'table
894 "create a link for to the table"
896 (let ((start (org-element-property :begin table))
897 (name (org-element-property :name table))
898 (caption (caaar (org-element-property :caption table))))
901 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]] %s\n"
902 c-b start counter (or name "") caption)
904 "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]]\n"
905 c-b start counter (or name ""))))))))
906 (switch-to-buffer "*List of Tables*")
907 (setq buffer-read-only nil)
910 (insert (mapconcat 'identity list-of-tables ""))
911 (setq buffer-read-only t)
912 (use-local-map (copy-keymap org-mode-map))
913 (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
917 'org-ref-list-of-tables
918 (lambda (keyword desc format)
921 (format "\\listoftables")))))
925 (defun org-ref-count-labels (label)
926 "Counts number of matches for LABEL in the document."
927 (+ (count-matches (format "label:%s\\b[^-:]" label) (point-min) (point-max))
928 ;; for tblname, it is not enough to get word boundary
929 ;; tab-little and tab-little-2 match then.
930 (count-matches (format "^#\\+tblname:\\s-*%s\\b[^-:]" label) (point-min) (point-max))
931 (count-matches (format "\\label{%s}" label) (point-min) (point-max))
932 ;; this is the org-format #+label:
933 (count-matches (format "^#\\+label:\\s-*%s\\b[^-:]" label) (point-min) (point-max))
934 (let ((custom-id-count 0))
937 (when (string= label (org-entry-get (point) "CUSTOM_ID"))
938 (setq custom-id-count (+ 1 custom-id-count)))))
944 "on clicking count the number of label tags used in the buffer. A number greater than one means multiple labels!"
945 (let ((count (org-ref-count-labels label)))
946 (message (format "%s occurence%s"
952 (org-ref-count-labels label))))
953 (lambda (keyword desc format)
955 ((eq format 'html) (format "(<label>%s</label>)" path))
957 (format "\\label{%s}" keyword)))))
959 (defun org-label-store-link ()
960 "Store a link to a label. The output will be a ref to that label."
961 ;; First we have to make sure we are on a label link.
962 (let* ((object (org-element-context)))
963 (when (and (equal (org-element-type object) 'link)
964 (equal (org-element-property :type object) "label"))
965 (org-store-link-props
967 :link (concat "ref:" (org-element-property :path object))))
969 ;; Store link on table
970 (when (equal (org-element-type object) 'table)
971 (org-store-link-props
973 :link (concat "ref:" (org-element-property :name object))))
975 ;; store link on heading with custom_id
976 ;; this is not a ref link, but it is still what you want
977 (when (and (equal (org-element-type object) 'headline)
978 (org-entry-get (point) "CUSTOM_ID"))
979 (org-store-link-props
981 :link (format "[[#%s]]" (org-entry-get (point) "CUSTOM_ID"))))
983 ;; and to #+label: lines
985 (when (and (equal (org-element-type object) 'paragraph)
986 (org-element-property :name object))
987 (org-store-link-props
989 :link (concat "ref:" (org-element-property :name object))))))
991 (add-hook 'org-store-link-functions 'org-label-store-link)
997 "on clicking goto the label. Navigate back with C-c &"
999 ;; next search from beginning of the buffer
1000 ;; it is possible you would not find the label if narrowing is in effect
1006 (goto-char (point-min))
1007 (re-search-forward (format "label:%s\\b" label) nil t))
1011 (goto-char (point-min))
1012 (re-search-forward (format "\\label{%s}" label) nil t))
1014 ;; #+label: name org-definition
1016 (goto-char (point-min))
1018 (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1022 (goto-char (point-min))
1024 (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t)))
1026 ;; we did not find anything, so go back to where we came
1027 (org-mark-ring-goto)
1028 (error "%s not found" label))
1030 (message "go back with (org-mark-ring-goto) `C-c &`"))
1032 (lambda (keyword desc format)
1034 ((eq format 'html) (format "(<ref>%s</ref>)" path))
1036 (format "\\ref{%s}" keyword)))))
1039 (defun org-ref-get-org-labels ()
1040 "Return a list of #+LABEL: labels."
1042 (goto-char (point-min))
1043 (let ((matches '()))
1044 (while (re-search-forward "^#\\+label:\\s-+\\(.*\\)\\b" (point-max) t)
1045 ;; do not do this for tables. We get those in `org-ref-get-tblnames'.
1046 ;; who would have thought you have save match data here? Trust me. When
1047 ;; I wrote this, you did.
1048 (unless (save-match-data (equal (car (org-element-at-point)) 'table))
1049 (add-to-list 'matches (match-string-no-properties 1) t)))
1053 (defun org-ref-get-custom-ids ()
1054 "Return a list of custom_id properties in the buffer."
1055 (let ((results '()) custom_id)
1058 (let ((custom_id (org-entry-get (point) "CUSTOM_ID")))
1059 (when (not (null custom_id))
1060 (setq results (append results (list custom_id)))))))
1064 (defun org-ref-get-latex-labels ()
1065 "Return list of matchin LaTeX defined labels in buffer."
1067 (goto-char (point-min))
1068 (let ((matches '()))
1069 (while (re-search-forward "\\\\label{\\([a-zA-z0-9:-]*\\)}" (point-max) t)
1070 (add-to-list 'matches (match-string-no-properties 1) t))
1074 (defun org-ref-get-tblnames ()
1075 "Return list of table names in the buffer."
1076 (org-element-map (org-element-parse-buffer 'element) 'table
1078 (org-element-property :name table))))
1081 (defun org-ref-get-labels ()
1082 "Return a list of labels in the buffer that you can make a ref link to.
1083 This is used to complete ref links and in helm menus."
1087 (goto-char (point-min))
1088 (let ((matches '()))
1089 ;; these are the org-ref label:stuff kinds
1090 (while (re-search-forward
1091 "[^#+]label:\\([a-zA-z0-9:-]*\\)" (point-max) t)
1092 (add-to-list 'matches (match-string-no-properties 1) t))
1093 ;; now add all the other kinds of labels.
1096 (org-ref-get-org-labels)
1098 (org-ref-get-latex-labels)
1099 ;; #+tblname: and actually #+label
1100 (org-ref-get-tblnames)
1102 (org-ref-get-custom-ids))))))
1105 (defun org-ref-helm-insert-label-link ()
1106 "Insert a label link. helm just shows you what labels already exist.
1107 If you are on a label link, replace it."
1109 (let* ((labels (org-ref-get-labels))
1110 (cb (current-buffer)))
1111 (helm :sources `(((name . "Existing labels")
1112 (candidates . ,labels)
1113 ;; default action is to open to the label
1114 (action . (lambda (label)
1115 ;; unfortunately I do not have markers here
1116 (org-open-link-from-string
1117 (format "ref:%s" label))))
1118 ;; if you select a label, replace current one
1119 (action . (lambda (label)
1120 (switch-to-buffer ,cb)
1122 ;; no prefix or on a link
1123 ((equal helm-current-prefix-arg nil)
1124 (let* ((object (org-element-context))
1125 (last-char (save-excursion
1126 (goto-char (org-element-property :end object))
1128 (if (looking-at " ")
1131 (when (-contains? '("label")
1132 (org-element-property :type object))
1133 ;; we are on a link, so replace it.
1136 (org-element-property :begin object)
1137 (org-element-property :end object))
1139 (replace-regexp-in-string
1140 (org-element-property :path object)
1142 (org-element-property :raw-link object))
1144 ;; no prefix options defined
1146 ;; no matching selection creates a new label
1147 ((name . "Create new label")
1149 ;; default action creates a new label, or replaces old one
1150 (action . (lambda (label)
1151 (switch-to-buffer ,cb)
1152 (let* ((object (org-element-context))
1153 (last-char (save-excursion
1154 (goto-char (org-element-property :end object))
1156 (if (looking-at " ")
1159 (if (-contains? '("label")
1160 (org-element-property :type object))
1161 ;; we are on a link, so replace it.
1164 (org-element-property :begin object)
1165 (org-element-property :end object))
1167 (replace-regexp-in-string
1168 (org-element-property :path object)
1170 (org-element-property :raw-link object))
1177 helm-pattern))))))))))))
1180 (defun org-ref-complete-link (&optional arg)
1181 "Completion function for ref links.
1182 Optional argument ARG Does nothing."
1184 (setq label (completing-read "label: " (org-ref-get-labels)))
1185 (format "ref:%s" label)))
1188 (defun org-ref-insert-ref-link ()
1189 "Completion function for a ref link."
1191 (insert (org-ref-complete-link)))
1194 (defun org-ref-helm-insert-ref-link ()
1195 "Helm menu to insert ref links to labels in the document.
1196 If you are on link, replace with newly selected label.
1197 Use C-u to insert a different kind of ref link.
1198 Use C-u C-u to insert a [[#custom-id]] link"
1200 (let* ((labels (org-ref-get-labels))
1201 (bs (buffer-string))
1202 (contexts (with-temp-buffer
1204 (mapcar 'org-ref-get-label-context labels)))
1205 (cb (current-buffer)))
1207 (helm :input (thing-at-point 'word)
1208 :sources `(((name . "Available labels to ref")
1209 (candidates . ,(loop for label in labels
1210 for context in contexts
1211 ;; we do some kludgy adding spaces
1212 ;; and bars to make it "easier" to
1214 collect (cons (concat
1219 (split-string context "\n")
1222 ;; default action to replace or insert ref link.
1223 (action . (lambda (label)
1224 (switch-to-buffer ,cb)
1227 ;; no prefix or on a link
1228 ((equal helm-current-prefix-arg nil)
1229 (let* ((object (org-element-context))
1230 (last-char (save-excursion
1231 (goto-char (org-element-property :end object))
1233 (if (looking-at " ")
1236 (if (-contains? '("ref" "eqref" "pageref" "nameref")
1237 (org-element-property :type object))
1238 ;; we are on a link, so replace it.
1241 (org-element-property :begin object)
1242 (org-element-property :end object))
1244 (replace-regexp-in-string
1245 (org-element-property :path object)
1247 (org-element-property :raw-link object))
1249 ;; insert a new link
1254 ;; one prefix, alternate ref link
1255 ((equal helm-current-prefix-arg '(4))
1258 (helm :sources '((name . "Ref link types")
1259 (candidates . ("ref" "eqref" "pageref" "nameref"))
1260 (action . (lambda (x) x))))
1262 ;; two prefixes, insert section custom-id link
1263 ((equal helm-current-prefix-arg '(16))
1265 (format "[[#%s]]" label)))
1273 "on clicking goto the label. Navigate back with C-c &"
1274 (org-mark-ring-push)
1275 ;; next search from beginning of the buffer
1281 (goto-char (point-min))
1282 (re-search-forward (format "label:%s\\b" label) nil t))
1286 (goto-char (point-min))
1287 (re-search-forward (format "\\label{%s}" label) nil t))
1289 ;; #+label: name org-definition
1291 (goto-char (point-min))
1293 (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1297 (goto-char (point-min))
1299 (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t)))
1300 ;; we did not find anything, so go back to where we came
1301 (org-mark-ring-goto)
1302 (error "%s not found" label))
1303 (message "go back with (org-mark-ring-goto) `C-c &`"))
1305 (lambda (keyword desc format)
1307 ((eq format 'html) (format "(<pageref>%s</pageref>)" path))
1309 (format "\\pageref{%s}" keyword)))))
1312 (defun org-pageref-complete-link (&optional arg)
1313 "Completion function for ref links.
1314 Optional argument ARG Does nothing."
1316 (setq label (completing-read "label: " (org-ref-get-labels)))
1317 (format "ref:%s" label)))
1320 (defun org-pageref-insert-ref-link ()
1321 "Insert a pageref link with completion."
1323 (insert (org-pageref-complete-link)))
1330 "on clicking goto the label. Navigate back with C-c &"
1331 (org-mark-ring-push)
1332 ;; next search from beginning of the buffer
1338 (goto-char (point-min))
1339 (re-search-forward (format "\\label{%s}" label) nil t))
1341 ;; we did not find anything, so go back to where we came
1342 (org-mark-ring-goto)
1343 (error "%s not found" label))
1344 (message "go back with (org-mark-ring-goto) `C-c &`"))
1346 (lambda (keyword desc format)
1348 ((eq format 'html) (format "(<nameref>%s</nameref>)" path))
1350 (format "\\nameref{%s}" keyword)))))
1357 "on clicking goto the label. Navigate back with C-c &"
1358 (org-mark-ring-push)
1359 ;; next search from beginning of the buffer
1361 (goto-char (point-min))
1364 ;; search forward for the first match
1366 (re-search-forward (format "label:%s" label) nil t)
1368 (re-search-forward (format "\\label{%s}" label) nil t)
1369 ;; #+label: name org-definition
1370 (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
1371 (org-mark-ring-goto)
1372 (error "%s not found" label))
1373 (message "go back with (org-mark-ring-goto) `C-c &`"))
1375 (lambda (keyword desc format)
1377 ((eq format 'html) (format "(<eqref>%s</eqref>)" path))
1379 (format "\\eqref{%s}" keyword)))))
1383 (defun org-ref-get-bibtex-key-under-cursor ()
1384 "Return key under the bibtex cursor.
1385 We search forward from
1386 point to get a comma, or the end of the link, and then backwards
1387 to get a comma, or the beginning of the link. that delimits the
1388 keyword we clicked on. We also strip the text properties."
1389 (let* ((object (org-element-context))
1390 (link-string (org-element-property :path object)))
1391 ;; you may click on the part before the citations. here we make
1392 ;; sure to move to the beginning so you get the first citation.
1394 (goto-char (org-element-property :begin object))
1395 (search-forward link-string (org-element-property :end object))
1396 (goto-char (match-beginning 0))
1397 ;; check if we clicked before the path and move as needed.
1398 (unless (< cp (point))
1401 (if (not (org-element-property :contents-begin object))
1402 ;; this means no description in the link
1404 ;; we need the link path start and end
1406 (goto-char (org-element-property :begin object))
1407 (search-forward link-string nil nil 1)
1408 (setq link-string-beginning (match-beginning 0))
1409 (setq link-string-end (match-end 0)))
1411 ;; The key is the text between commas, or the link boundaries
1413 (if (search-forward "," link-string-end t 1)
1414 (setq key-end (- (match-end 0) 1)) ; we found a match
1415 (setq key-end link-string-end))) ; no comma found so take the end
1416 ;; and backward to previous comma from point which defines the start character
1418 (if (search-backward "," link-string-beginning 1 1)
1419 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
1420 (setq key-beginning link-string-beginning))) ; no match found
1421 ;; save the key we clicked on.
1423 (org-ref-strip-string
1424 (buffer-substring key-beginning key-end)))
1425 (set-text-properties 0 (length bibtex-key) nil bibtex-key)
1427 ;; link with description. assume only one key
1430 (defun org-ref-find-bibliography ()
1431 "Find the bibliography in the buffer.
1432 This function sets and returns cite-bibliography-files, which is a list of files
1433 either from bibliography:f1.bib,f2.bib
1434 \bibliography{f1,f2}
1435 internal bibliographies
1437 falling back to what the user has set in `org-ref-default-bibliography'"
1440 (goto-char (point-min))
1441 ;; look for a bibliography link
1442 (when (re-search-forward "\\<bibliography:\\([^\]\|\n]+\\)" nil t)
1443 (setq org-ref-bibliography-files
1444 (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
1445 (throw 'result org-ref-bibliography-files))
1448 ;; we did not find a bibliography link. now look for \bibliography
1449 (goto-char (point-min))
1450 (when (re-search-forward "\\\\bibliography{\\([^}]+\\)}" nil t)
1451 ;; split, and add .bib to each file
1452 (setq org-ref-bibliography-files
1453 (mapcar (lambda (x) (concat x ".bib"))
1454 (mapcar 'org-ref-strip-string
1455 (split-string (match-string 1) ","))))
1456 (throw 'result org-ref-bibliography-files))
1458 ;; no bibliography found. maybe we need a biblatex addbibresource
1459 (goto-char (point-min))
1460 ;; look for a bibliography link
1461 (when (re-search-forward "addbibresource:\\([^\]\|\n]+\\)" nil t)
1462 (setq org-ref-bibliography-files
1463 (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
1464 (throw 'result org-ref-bibliography-files))
1466 ;; we did not find anything. use defaults
1467 (setq org-ref-bibliography-files org-ref-default-bibliography)))
1469 ;; set reftex-default-bibliography so we can search
1470 (set (make-local-variable 'reftex-default-bibliography) org-ref-bibliography-files)
1471 org-ref-bibliography-files)
1473 (defun org-ref-key-in-file-p (key filename)
1474 "Determine if the KEY is in the FILENAME."
1475 (save-current-buffer
1476 (let ((bibtex-files (list filename)))
1477 ;; This is something I am trying because when the bibtex file is open, and
1478 ;; you have added to it, the only way I find to get the update to update
1479 ;; is to close it and reopen it. or to save it and revert it.
1480 (when (get-file-buffer filename)
1481 (set-buffer (get-file-buffer filename))
1483 (revert-buffer t t))
1484 (bibtex-search-entry key t))))
1486 (defun org-ref-get-bibtex-key-and-file (&optional key)
1487 "Return the bibtex KEY and file that it is in. If no key is provided, get one under point."
1488 (let ((org-ref-bibliography-files (org-ref-find-bibliography))
1491 (setq key (org-ref-get-bibtex-key-under-cursor)))
1492 (setq file (catch 'result
1493 (loop for file in org-ref-bibliography-files do
1494 (if (org-ref-key-in-file-p key (file-truename file))
1495 (throw 'result file)))))
1498 ;; *** key at point functions
1500 (defun org-ref-open-pdf-at-point ()
1501 "Open the pdf for bibtex key under point if it exists."
1503 (let* ((results (org-ref-get-bibtex-key-and-file))
1505 (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key)))
1506 (if (file-exists-p pdf-file)
1507 (org-open-file pdf-file)
1508 (message "no pdf found for %s" key))))
1511 (defun org-ref-open-url-at-point ()
1512 "Open the url for bibtex key under point."
1514 (let* ((results (org-ref-get-bibtex-key-and-file))
1516 (bibfile (cdr results)))
1519 (insert-file-contents bibfile)
1520 (bibtex-search-entry key)
1521 ;; I like this better than bibtex-url which does not always find
1524 (let ((url (bibtex-autokey-get-field "url")))
1526 (browse-url (s-trim url))
1529 (let ((doi (bibtex-autokey-get-field "doi")))
1531 (if (string-match "^http" doi)
1533 (browse-url (format "http://dx.doi.org/%s" (s-trim doi))))
1534 (throw 'done nil))))))))
1537 (defun org-ref-open-notes-at-point ()
1538 "Open the notes for bibtex key under point."
1540 (let* ((results (org-ref-get-bibtex-key-and-file))
1542 (bibfile (cdr results)))
1545 (insert-file-contents bibfile)
1546 (bibtex-search-entry key)
1547 (org-ref-open-bibtex-notes)))))
1550 (defun org-ref-citation-at-point ()
1551 "Give message of current citation at point."
1553 (let* ((cb (current-buffer))
1554 (results (org-ref-get-bibtex-key-and-file))
1556 (bibfile (cdr results)))
1557 (message "%s" (progn
1559 (insert-file-contents bibfile)
1560 (bibtex-search-entry key)
1561 (org-ref-bib-citation))))))
1564 (defun org-ref-open-citation-at-point ()
1565 "Open bibtex file to key at point."
1567 (let* ((cb (current-buffer))
1568 (results (org-ref-get-bibtex-key-and-file))
1570 (bibfile (cdr results)))
1572 (bibtex-search-entry key)))
1576 (defvar org-ref-cite-menu-funcs '()
1577 "Functions to run on cite click menu.
1578 Each entry is a list of (key menu-name function).
1579 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.")
1582 (defvar org-ref-user-cite-menu-funcs
1583 '(("C" "rossref" org-ref-crossref-at-point)
1584 ("y" "Copy entry to file" org-ref-copy-entry-at-point-to-file)
1585 ("s" "Copy summary" org-ref-copy-entry-as-summary))
1586 "User-defined functions to run on bibtex key at point.")
1589 (defun org-ref-copy-entry-as-summary ()
1590 "Copy the bibtex entry for the citation at point as a summary."
1592 (save-window-excursion
1593 (org-ref-open-citation-at-point)
1594 (kill-new (org-ref-bib-citation))))
1597 (defun org-ref-copy-entry-at-point-to-file ()
1598 "Copy the bibtex entry for the citation at point to NEW-FILE.
1599 Prompt for NEW-FILE includes bib files in `org-ref-default-bibliography', and bib files in current working directory. You can also specify a new file."
1601 (let ((new-file (ido-completing-read
1603 (append org-ref-default-bibliography
1604 (f-entries "." (lambda (f) (f-ext? f "bib"))))))
1605 (key (org-ref-get-bibtex-key-under-cursor)))
1606 (save-window-excursion
1607 (org-ref-open-citation-at-point)
1608 (bibtex-copy-entry-as-kill))
1610 (let ((bibtex-files (list (file-truename new-file))))
1611 (if (assoc key (bibtex-global-key-alist))
1612 (message "That key already exists in %s" new-file)
1614 (save-window-excursion
1615 (find-file new-file)
1616 (goto-char (point-max))
1617 ;; make sure we are at the beginning of a line.
1618 (unless (looking-at "^") (insert "\n\n"))
1623 (defun org-ref-get-doi-at-point ()
1624 "Get doi for key at point."
1625 (let* ((results (org-ref-get-bibtex-key-and-file))
1627 (bibfile (cdr results))
1631 (insert-file-contents bibfile)
1632 (bibtex-search-entry key)
1633 (setq doi (bibtex-autokey-get-field "doi"))
1634 ;; in case doi is a url, remove the url part.
1635 (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))))
1638 ;; **** functions that operate on key at point for click menu
1639 (defun org-ref-wos-at-point ()
1640 "Open the doi in wos for bibtex key under point."
1642 (doi-utils-wos (org-ref-get-doi-at-point)))
1645 (defun org-ref-wos-citing-at-point ()
1646 "Open the doi in wos citing articles for bibtex key under point."
1648 (doi-utils-wos-citing (org-ref-get-doi-at-point)))
1651 (defun org-ref-wos-related-at-point ()
1652 "Open the doi in wos related articles for bibtex key under point."
1654 (doi-utils-wos-related (org-ref-get-doi-at-point)))
1657 (defun org-ref-google-scholar-at-point ()
1658 "Open the doi in google scholar for bibtex key under point."
1660 (doi-utils-google-scholar (org-ref-get-doi-at-point)))
1663 (defun org-ref-pubmed-at-point ()
1664 "Open the doi in pubmed for bibtex key under point."
1666 (doi-utils-pubmed (org-ref-get-doi-at-point)))
1669 (defun org-ref-crossref-at-point ()
1670 "Open the doi in crossref for bibtex key under point."
1672 (doi-utils-crossref (org-ref-get-doi-at-point)))
1674 ;; *** Minibuffer menu
1676 (defun org-ref-cite-onclick-minibuffer-menu (&optional link-string)
1677 "Action when a cite link is clicked on.
1678 Provides a menu of context sensitive actions. If the bibtex entry
1679 has a pdf, you get an option to open it. If there is a doi, you
1680 get a lot of options. LINK-STRING is used by the link function."
1682 (let* ((results (org-ref-get-bibtex-key-and-file))
1684 (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
1685 (bibfile (cdr results))
1686 (url (save-excursion
1688 (insert-file-contents bibfile)
1689 (bibtex-search-entry key)
1690 (bibtex-autokey-get-field "url"))))
1691 (doi (save-excursion
1693 (insert-file-contents bibfile)
1694 (bibtex-search-entry key)
1695 ;; I like this better than bibtex-url which does not always find
1697 (bibtex-autokey-get-field "doi")))))
1699 (when (string= "" doi) (setq doi nil))
1700 (when (string= "" url) (setq url nil))
1701 (setq org-ref-cite-menu-funcs '())
1707 'org-ref-cite-menu-funcs
1708 '("o" "pen" org-ref-open-citation-at-point)))
1711 (when (file-exists-p pdf-file)
1713 'org-ref-cite-menu-funcs
1714 `("p" "df" ,org-ref-open-pdf-function) t))
1718 'org-ref-cite-menu-funcs
1719 '("n" "otes" org-ref-open-notes-at-point) t)
1724 'org-ref-cite-menu-funcs
1725 '("u" "rl" org-ref-open-url-at-point) t))
1730 'org-ref-cite-menu-funcs
1731 '("w" "os" org-ref-wos-at-point) t)
1734 'org-ref-cite-menu-funcs
1735 '("c" "iting" org-ref-wos-citing-at-point) t)
1738 'org-ref-cite-menu-funcs
1739 '("r" "elated" org-ref-wos-related-at-point) t)
1742 'org-ref-cite-menu-funcs
1743 '("g" "oogle scholar" org-ref-google-scholar-at-point) t)
1746 'org-ref-cite-menu-funcs
1747 '("P" "ubmed" org-ref-pubmed-at-point) t))
1749 ;; add user functions
1750 (dolist (tup org-ref-user-cite-menu-funcs)
1752 'org-ref-cite-menu-funcs
1757 'org-ref-cite-menu-funcs
1758 '("q" "uit" (lambda ())) t)
1760 ;; now we make a menu
1761 ;; construct menu string as a message
1764 (let* ((results (org-ref-get-bibtex-key-and-file))
1766 (bibfile (cdr results)))
1769 (insert-file-contents bibfile)
1770 (bibtex-search-entry key)
1771 (org-ref-bib-citation))))
1775 (concat "[" (elt tup 0) "]"
1777 org-ref-cite-menu-funcs "")))
1779 (let* ((input (read-char-exclusive))
1781 (char-to-string input) org-ref-cite-menu-funcs)))
1782 ;; now run the function (2nd element in choice)
1789 ;; *** Generation of the cite links
1790 (defmacro org-ref-make-completion-function (type)
1791 "Macro to make a link completion function for a link of TYPE."
1792 `(defun ,(intern (format "org-%s-complete-link" type)) (&optional arg)
1798 (let ((bibtex-files (org-ref-find-bibliography)))
1799 (bibtex-global-key-alist))))))
1801 (defmacro org-ref-make-format-function (type)
1802 "Macro to make a format function for a link of TYPE."
1803 `(defun ,(intern (format "org-ref-format-%s" type)) (keyword desc format)
1808 (format "[[#%s][%s]]" key key))
1809 (org-ref-split-and-strip-string keyword) ","))
1816 (org-ref-split-and-strip-string keyword) ",") "]"))
1821 (format "<a href=\"#%s\">%s</a>" key key))
1822 (org-ref-split-and-strip-string keyword) ","))
1825 (if (string= (substring type -1) "s")
1826 ;; biblatex format for multicite commands, which all end in s. These are formated as \cites{key1}{key2}...
1827 (concat "\\" ,type (mapconcat (lambda (key) (format "{%s}" key))
1828 (org-ref-split-and-strip-string keyword) ""))
1830 (concat "\\" ,type (when desc (org-ref-format-citation-description desc)) "{"
1831 (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
1833 ;; for markdown we generate pandoc citations
1836 (desc ;; pre and or post text
1837 (let* ((text (split-string desc "::"))
1841 (format "[@%s," keyword)
1842 (when pre (format " %s" pre))
1843 (when post (format ", %s" post))
1848 (lambda (key) (concat "@" key))
1849 (org-ref-split-and-strip-string keyword)
1852 (defun org-ref-format-citation-description (desc)
1853 "Return formatted citation description.
1854 If the cite link has a DESC (description), it is optional text
1855 for the citation command. You can specify pre and post text by
1856 separating these with ::, for example [[cite:key][pre text::post
1859 ((string-match "::" desc)
1860 (format "[%s][%s]" (car (setq results (split-string desc "::"))) (cadr results)))
1861 (t (format "[%s]" desc))))
1863 (defun org-ref-define-citation-link (type &optional key)
1864 "Add a citation link of TYPE for org-ref.
1865 With optional KEY, set the reftex binding. For example:
1866 \(org-ref-define-citation-link \"citez\" ?z) will create a new
1867 citez link, with reftex key of z, and the completion function."
1868 (interactive "sCitation Type: \ncKey: ")
1870 ;; create the formatting function
1871 (eval `(org-ref-make-format-function ,type))
1876 org-ref-cite-onclick-function
1877 (quote ,(intern (format "org-ref-format-%s" type)))))
1879 ;; create the completion function
1880 (eval `(org-ref-make-completion-function ,type))
1882 ;; store new type so it works with adding citations, which checks
1883 ;; for existence in this list
1884 (add-to-list 'org-ref-cite-types type)
1886 ;; and finally if a key is specified, we modify the reftex menu
1888 (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
1889 (append (nth 2 (assoc 'org reftex-cite-format-builtin))
1890 `((,key . ,(concat type ":%l")))))))
1892 ;; create all the link types and their completion functions
1893 (mapcar 'org-ref-define-citation-link org-ref-cite-types)
1895 (defun org-ref-insert-cite-link (alternative-cite)
1896 "Insert a default citation link using reftex.
1897 If you are on a link, it appends to the end of the link,
1898 otherwise, a new link is inserted. Use a prefix
1899 arg (ALTERNATIVE-CITE) to get a menu of citation types."
1901 (org-ref-find-bibliography)
1902 (let* ((object (org-element-context))
1903 (link-string-beginning (org-element-property :begin object))
1904 (link-string-end (org-element-property :end object))
1905 (path (org-element-property :path object)))
1907 (if (not alternative-cite)
1910 ;; case where we are in a link
1911 ((and (equal (org-element-type object) 'link)
1912 (-contains? org-ref-cite-types (org-element-property :type object)))
1913 (goto-char link-string-end)
1914 ;; sometimes there are spaces at the end of the link
1915 ;; this code moves point pack until no spaces are there
1916 (while (looking-back " ") (backward-char))
1917 (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
1919 ;; We are next to a link, and we want to append
1922 (and (equal (org-element-type (org-element-context)) 'link)
1923 (-contains? org-ref-cite-types (org-element-property :type (org-element-context)))))
1924 (while (looking-back " ") (backward-char))
1925 (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
1927 ;; insert fresh link
1930 (concat org-ref-default-citation-link
1932 (mapconcat 'identity (reftex-citation t) ",")))))
1934 ;; you pressed a C-u so we run this code
1935 (reftex-citation))))
1937 (defun org-ref-insert-cite-with-completion (type)
1938 "Insert a cite link of TYPE with completion."
1939 (interactive (list (ido-completing-read "Type: " org-ref-cite-types)))
1940 (insert (funcall (intern (format "org-%s-complete-link" type)))))
1942 (defun org-ref-store-bibtex-entry-link ()
1943 "Save a citation link to the current bibtex entry. Save in the default link type."
1945 (let ((link (concat org-ref-default-citation-link
1948 (bibtex-beginning-of-entry)
1949 (reftex-get-bib-field "=key=" (bibtex-parse-entry))))))
1950 (message "saved %s" link)
1951 (push (list link) org-stored-links)
1952 (car org-stored-links)))
1960 (lambda (path desc format)
1963 (format "\\index{%s}" path)))))
1965 ;; this will generate a temporary index of entries in the file.
1969 (let ((*index-links* '())
1970 (*initial-letters* '()))
1973 (org-element-map (org-element-parse-buffer) 'link
1975 (let ((type (nth 0 link))
1976 (plist (nth 1 link)))
1978 (when (equal (plist-get plist ':type) "index")
1981 (cons (plist-get plist :path)
1983 "[[elisp:(progn (switch-to-buffer \"%s\") (goto-char %s))][%s]]"
1985 (plist-get plist :begin) ;; position of link
1986 ;; grab a description
1988 (goto-char (plist-get plist :begin))
1989 (if (thing-at-point 'sentence)
1991 (replace-regexp-in-string
1992 "\n" "" (thing-at-point 'sentence))
1993 ;; or call it a link
1997 (setq *index-links* (cl-sort *index-links* 'string-lessp :key 'car))
1999 ;; now first letters
2000 (dolist (link *index-links*)
2001 (add-to-list '*initial-letters* (substring (car link) 0 1) t))
2003 ;; now create the index
2004 (switch-to-buffer (get-buffer-create "*index*"))
2007 (insert "#+TITLE: Index\n\n")
2008 (dolist (letter *initial-letters*)
2009 (insert (format "* %s\n" (upcase letter)))
2010 ;; now process the links
2013 (string= letter (substring (car (car *index-links*)) 0 1)))
2014 (let ((link (pop *index-links*)))
2015 (insert (format "%s %s\n\n" (car link) (cdr link))))))
2016 (switch-to-buffer "*index*")))
2018 (lambda (path desc format)
2021 (format "\\printindex")))))
2026 nil ;; no follow action
2027 (lambda (path desc format)
2030 (format "\\newglossaryentry{%s}{%s}" path desc)))))
2036 nil ;; no follow action
2037 (lambda (path desc format)
2040 (format "\\gls{%s}" path)))))
2045 nil ;; no follow action
2046 (lambda (path desc format)
2049 (format "\\glspl{%s}" path)))))
2054 nil ;; no follow action
2055 (lambda (path desc format)
2058 (format "\\Gls{%s}" path)))))
2063 nil ;; no follow action
2064 (lambda (path desc format)
2067 (format "\\Glspl{%s}" path)))))
2070 ;; ** create text citations from a bibtex entry
2071 (defun org-ref-bib-citation ()
2072 "From a bibtex entry, create and return a simple citation string.
2073 This assumes you are in an article."
2075 (bibtex-beginning-of-entry)
2076 (let* ((cb (current-buffer))
2077 (bibtex-expand-strings t)
2078 (entry (loop for (key . value) in (bibtex-parse-entry t)
2079 collect (cons (downcase key) value)))
2080 (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2081 (year (reftex-get-bib-field "year" entry))
2082 (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2083 (key (reftex-get-bib-field "=key=" entry))
2084 (journal (reftex-get-bib-field "journal" entry))
2085 (volume (reftex-get-bib-field "volume" entry))
2086 (pages (reftex-get-bib-field "pages" entry))
2087 (doi (reftex-get-bib-field "doi" entry))
2088 (url (reftex-get-bib-field "url" entry))
2090 ;;authors, "title", Journal, vol(iss):pages (year).
2091 (format "%s, \"%s\", %s, %s:%s (%s)"
2092 author title journal volume pages year)))
2094 (defun org-ref-bib-html-citation ()
2095 "From a bibtex entry, create and return a simple citation with html links."
2096 (bibtex-beginning-of-entry)
2097 (let* ((cb (current-buffer))
2098 (bibtex-expand-strings t)
2099 (entry (loop for (key . value) in (bibtex-parse-entry t)
2100 collect (cons (downcase key) value)))
2101 (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2102 (year (reftex-get-bib-field "year" entry))
2103 (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2104 (key (reftex-get-bib-field "=key=" entry))
2105 (journal (reftex-get-bib-field "journal" entry))
2106 (volume (reftex-get-bib-field "volume" entry))
2107 (pages (reftex-get-bib-field "pages" entry))
2108 (doi (reftex-get-bib-field "doi" entry))
2109 (url (reftex-get-bib-field "url" entry)))
2110 ;;authors, "title", Journal, vol(iss):pages (year).
2111 (concat (format "%s, \"%s\", %s, %s:%s (%s)."
2112 author title journal volume pages year)
2113 (when url (format " <a href=\"%s\">link</a>" url))
2115 (format " <a href=\"http://dx.doi.org/%s\">doi</a>" doi)))))
2117 ;; ** Open pdf in bibtex entry
2118 (defun org-ref-open-bibtex-pdf ()
2119 "Open pdf for a bibtex entry, if it exists.
2121 the entry of interest in the bibfile. but does not check that."
2124 (bibtex-beginning-of-entry)
2125 (let* ((bibtex-expand-strings t)
2126 (entry (bibtex-parse-entry t))
2127 (key (reftex-get-bib-field "=key=" entry))
2128 (pdf (format (concat org-ref-pdf-directory "%s.pdf") key)))
2130 (if (file-exists-p pdf)
2131 (org-open-link-from-string (format "[[file:%s]]" pdf))
2134 ;; ** Open notes from bibtex entry
2136 (defun org-ref-open-bibtex-notes ()
2137 "From a bibtex entry, open the notes if they exist, and create a heading if they do not.
2139 I never did figure out how to use reftex to make this happen
2140 non-interactively. the reftex-format-citation function did not
2141 work perfectly; there were carriage returns in the strings, and
2142 it did not put the key where it needed to be. so, below I replace
2143 the carriage returns and extra spaces with a single space and
2144 construct the heading by hand."
2147 (bibtex-beginning-of-entry)
2148 (let* ((cb (current-buffer))
2149 (bibtex-expand-strings t)
2150 (entry (loop for (key . value) in (bibtex-parse-entry t)
2151 collect (cons (downcase key) value)))
2152 (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
2153 (year (reftex-get-bib-field "year" entry))
2154 (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
2155 (key (reftex-get-bib-field "=key=" entry))
2156 (journal (reftex-get-bib-field "journal" entry))
2157 (volume (reftex-get-bib-field "volume" entry))
2158 (pages (reftex-get-bib-field "pages" entry))
2159 (doi (reftex-get-bib-field "doi" entry))
2160 (url (reftex-get-bib-field "url" entry))
2163 ;; save key to clipboard to make saving pdf later easier by pasting.
2166 (kill-ring-save (point-min) (point-max)))
2168 ;; now look for entry in the notes file
2169 (if org-ref-bibliography-notes
2170 (find-file-other-window org-ref-bibliography-notes)
2171 (error "Org-ref-bib-bibliography-notes is not set to anything"))
2173 (goto-char (point-min))
2174 ;; put new entry in notes if we don't find it.
2175 (if (re-search-forward (format ":Custom_ID: %s$" key) nil 'end)
2176 (funcall org-ref-open-notes-function)
2177 ;; no entry found, so add one
2178 (insert (format "\n** TODO %s - %s" year title))
2190 [[cite:%s]] [[file:%s/%s.pdf][pdf]]\n\n"
2191 key author journal year volume pages doi url key org-ref-pdf-directory key))
2194 (defun org-ref-open-notes-from-reftex ()
2195 "Call reftex, and open notes for selected entry."
2197 (let ((bibtex-key )))
2199 ;; now look for entry in the notes file
2200 (if org-ref-bibliography-notes
2201 (find-file-other-window org-ref-bibliography-notes)
2202 (error "Org-ref-bib-bibliography-notes is not set to anything"))
2204 (goto-char (point-min))
2206 (re-search-forward (format
2208 (first (reftex-citation t)) nil 'end))
2209 (funcall org-ref-open-notes-function))
2211 ;; ** Open bibtex entry in browser
2212 (defun org-ref-open-in-browser ()
2213 "Open the bibtex entry at point in a browser using the url field or doi field."
2216 (bibtex-beginning-of-entry)
2218 (let ((url (bibtex-autokey-get-field "url")))
2223 (let ((doi (bibtex-autokey-get-field "doi")))
2225 (if (string-match "^http" doi)
2227 (browse-url (format "http://dx.doi.org/%s" doi)))
2229 (message "No url or doi found"))))
2231 ;; ** upload entry to citeulike
2233 (defun org-ref-upload-bibtex-entry-to-citeulike ()
2234 "With point in a bibtex entry get bibtex string and submit to citeulike.
2236 Relies on the python script /upload_bibtex_citeulike.py being in the user directory."
2238 (message "uploading to citeulike")
2240 (bibtex-narrow-to-entry)
2241 (let ((startpos (point-min))
2242 (endpos (point-max))
2243 (bibtex-string (buffer-string))
2244 (script (concat "python " starter-kit-dir "/upload_bibtex_citeulike.py&")))
2245 (with-temp-buffer (insert bibtex-string)
2246 (shell-command-on-region (point-min) (point-max) script t nil nil t)))))
2248 ;; ** Build a pdf of the bibtex file
2249 (defun org-ref-build-full-bibliography ()
2250 "Build pdf of all bibtex entries, and open it."
2252 (let* ((bibfile (file-name-nondirectory (buffer-file-name)))
2253 (bib-base (file-name-sans-extension bibfile))
2254 (texfile (concat bib-base ".tex"))
2255 (pdffile (concat bib-base ".pdf")))
2258 (insert (format "\\documentclass[12pt]{article}
2259 \\usepackage[version=3]{mhchem}
2261 \\usepackage[numbers]{natbib}
2262 \\usepackage[colorlinks=true, linkcolor=blue, urlcolor=blue, pdfstartview=FitH]{hyperref}
2266 \\bibliographystyle{unsrtnat}
2268 \\end{document}" bib-base))
2270 (shell-command (concat "pdflatex " bib-base))
2271 (shell-command (concat "bibtex " bib-base))
2272 (shell-command (concat "pdflatex " bib-base))
2273 (shell-command (concat "pdflatex " bib-base))
2274 (kill-buffer texfile)
2275 (org-open-file pdffile)
2278 ;; ** Extract bibtex entries in org-file
2280 (defun org-ref-extract-bibtex-entries ()
2281 "Extract the bibtex entries referred to by cite links in the current buffer into a src block at the bottom of the current buffer.
2283 If no bibliography is in the buffer the variable
2284 `reftex-default-bibliography' is used."
2286 (let* ((temporary-file-directory (file-name-directory (buffer-file-name)))
2287 (tempname (make-temp-file "extract-bib"))
2288 (contents (buffer-string))
2289 (cb (current-buffer))
2290 basename texfile bibfile results)
2292 ;; open tempfile and insert org-buffer contents
2293 (find-file tempname)
2295 (setq basename (file-name-sans-extension
2296 (file-name-nondirectory buffer-file-name))
2297 texfile (concat tempname ".tex")
2298 bibfile (concat tempname ".bib"))
2300 ;; see if we have a bibliography, and insert the default one if not.
2302 (goto-char (point-min))
2303 (unless (re-search-forward "^bibliography:" (point-max) 'end)
2304 (insert (format "\nbibliography:%s"
2305 (mapconcat 'identity reftex-default-bibliography ",")))))
2308 ;; get a latex file and extract the references
2309 (org-latex-export-to-latex)
2312 (reftex-create-bibtex-file bibfile)
2314 ;; save results of the references
2315 (setq results (buffer-string))
2317 ;; kill buffers. these are named by basename, not full path
2318 (kill-buffer (concat basename ".bib"))
2319 (kill-buffer (concat basename ".tex"))
2320 (kill-buffer basename)
2322 (delete-file bibfile)
2323 (delete-file texfile)
2324 (delete-file tempname)
2326 ;; Now back to the original org buffer and insert the results
2327 (switch-to-buffer cb)
2328 (when (not (string= "" results))
2330 (goto-char (point-max))
2332 (org-insert-heading)
2333 (insert (format " Bibtex entries
2335 #+BEGIN_SRC text :tangle %s
2337 #+END_SRC" (concat (file-name-sans-extension (file-name-nondirectory (buffer-file-name))) ".bib") results))))))
2339 ;; ** Find bad citations
2342 (defun index (substring list)
2343 "Return the index of SUBSTRING in a LIST of strings."
2346 (dolist (arg list i)
2347 (if (string-match (concat "^" substring "$") arg)
2352 ;; return counter if found, otherwise return nil
2356 (defun org-ref-find-bad-citations ()
2357 "Create a list of citation keys in an org-file that do not have a bibtex entry in the known bibtex files.
2359 Makes a new buffer with clickable links."
2361 ;; generate the list of bibtex-keys and cited keys
2362 (let* ((bibtex-files (org-ref-find-bibliography))
2363 (bibtex-file-path (mapconcat (lambda (x) (file-name-directory (file-truename x))) bibtex-files ":"))
2364 (bibtex-keys (mapcar (lambda (x) (car x)) (bibtex-global-key-alist)))
2365 (bad-citations '()))
2367 (org-element-map (org-element-parse-buffer) 'link
2369 (let ((plist (nth 1 link)))
2370 (when (-contains? org-ref-cite-types (plist-get plist :type))
2371 (dolist (key (org-ref-split-and-strip-string (plist-get plist :path)))
2372 (when (not (index key bibtex-keys))
2377 `(,(format "%s [[elisp:(progn (switch-to-buffer-other-frame \"%s\")(goto-char %s))][not found here]]\n"
2380 (plist-get plist :begin)))))
2382 ;; set with-affilates to t to get citations in a caption
2387 (switch-to-buffer-other-window "*Missing citations*")
2390 (insert "* List of bad cite links\n")
2391 (insert (mapconcat 'identity bad-citations ""))
2392 ;(setq buffer-read-only t)
2393 (use-local-map (copy-keymap org-mode-map))
2394 (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))
2396 (when (get-buffer "*Missing citations*")
2397 (kill-buffer "*Missing citations*"))
2398 (message "No bad cite links found"))))
2400 ;; ** helm interface to bad citations, labels, refs and files in orgfile
2401 (defun org-ref-bad-cite-candidates ()
2402 "Return a list of conses (key . marker) where key does not exist in the known bibliography files, and marker points to the key."
2403 (let* ((cp (point)) ; save to return to later
2404 (bibtex-files (org-ref-find-bibliography))
2405 (bibtex-file-path (mapconcat
2407 (file-name-directory (file-truename x)))
2409 (bibtex-keys (mapcar (lambda (x) (car x))
2410 (bibtex-global-key-alist)))
2411 (bad-citations '()))
2413 (org-element-map (org-element-parse-buffer) 'link
2415 (let ((plist (nth 1 link)))
2416 (when (-contains? org-ref-cite-types (plist-get plist :type))
2417 (dolist (key (org-ref-split-and-strip-string (plist-get plist :path)) )
2418 (when (not (index key bibtex-keys))
2419 (goto-char (plist-get plist :begin))
2420 (re-search-forward key)
2421 (push (cons key (point-marker)) bad-citations)))
2423 ;; add with-affiliates to get cites in caption
2429 (defun org-ref-bad-ref-candidates ()
2430 "Return a list of conses (ref . marker) where ref is a ref link that does not point to anything (i.e. a label)."
2431 ;; first get a list of legitimate labels
2433 (labels (org-ref-get-labels))
2435 ;; now loop over ref links
2436 (goto-char (point-min))
2437 (org-element-map (org-element-parse-buffer) 'link
2439 (let ((plist (nth 1 link)))
2440 (when (or (equal (plist-get plist ':type) "ref")
2441 (equal (plist-get plist ':type) "eqref")
2442 (equal (plist-get plist ':type) "pageref")
2443 (equal (plist-get plist ':type) "nameref"))
2444 (unless (-contains? labels (plist-get plist :path))
2445 (goto-char (plist-get plist :begin))
2448 (cons (plist-get plist :path)
2449 (point-marker))))))))
2454 (defun org-ref-bad-label-candidates ()
2455 "Return a list of labels where label is multiply defined."
2456 (let ((labels (org-ref-get-labels))
2457 (multiple-labels '()))
2458 (when (not (= (length labels)
2459 (length (-uniq labels))))
2460 (dolist (label labels)
2461 (when (> (-count (lambda (a)
2464 ;; this is a multiply defined label.
2466 (goto-char (point-min))
2467 (while (re-search-forward
2468 (format "[^#+]label:%s\\s-" label) nil t)
2469 (push (cons label (point-marker)) multiple-labels))
2470 (goto-char (point-min))
2471 (while (re-search-forward
2472 (format "\\label{%s}\\s-?" label) nil t)
2473 (push (cons label (point-marker)) multiple-labels))
2475 (goto-char (point-min))
2476 (while (re-search-forward
2477 (format "^#\\+label:\\s-*%s" label) nil t)
2478 (push (cons label (point-marker)) multiple-labels))
2480 (goto-char (point-min))
2481 (while (re-search-forward
2482 (format "^#\\+tblname:\\s-*%s" label) nil t)
2483 (push (cons label (point-marker)) multiple-labels))
2487 (defun org-ref-bad-file-link-candidates ()
2488 "Return list of conses (link . marker) wehre the file in the link does not exist."
2489 (let* ((bad-files '()))
2490 (org-element-map (org-element-parse-buffer) 'link
2492 (let ((type (org-element-property :type link)))
2493 (when (or (string= "file" type)
2494 (string= "attachfile" type))
2495 (unless (file-exists-p (org-element-property :path link))
2496 (add-to-list 'bad-files
2497 (cons (org-element-property :path link)
2500 (org-element-property :begin link))
2501 (point-marker)))))))))
2502 ;; Let us also check \attachfile{fname}
2504 (goto-char (point-min))
2505 (while (re-search-forward "\\attachfile{\\(.*\\)}" nil t)
2506 (unless (file-exists-p (match-string 1))
2507 (add-to-list 'bad-files (cons (match-string 1) (point-marker))))))
2512 "Opens a helm interface to actions for org-ref.
2513 Shows bad citations, ref links and labels"
2515 (let ((cb (current-buffer))
2516 (bad-citations (org-ref-bad-cite-candidates))
2517 (bad-refs (org-ref-bad-ref-candidates))
2518 (bad-labels (org-ref-bad-label-candidates))
2519 (bad-files (org-ref-bad-file-link-candidates)))
2521 (helm :sources `(((name . "Bad citations")
2522 (candidates . ,bad-citations)
2523 (action . (lambda (marker)
2524 (switch-to-buffer (marker-buffer marker))
2525 (goto-char marker))))
2527 ((name . "Bad Labels")
2528 (candidates . ,bad-labels)
2529 (action . (lambda (marker)
2530 (switch-to-buffer (marker-buffer marker))
2531 (goto-char marker))))
2533 ((name . "Bad ref links")
2534 (candidates . ,bad-refs)
2535 (action . (lambda (marker)
2536 (switch-to-buffer (marker-buffer marker))
2537 (goto-char marker))))
2539 ((name . "Bad file links")
2540 (candidates . ,bad-files)
2542 (switch-to-buffer (marker-buffer marker))
2543 (goto-char marker)))
2545 ((name . "Utilities")
2546 (candidates . (("Check buffer again" . org-ref)
2547 ("Insert citation" . helm-bibtex)
2548 ("Insert label link" . org-ref-helm-insert-label-link)
2549 ("Insert ref link" . org-ref-helm-insert-ref-link)
2550 ("List of figures" . org-ref-list-of-figures)
2551 ("List of tables" . org-ref-list-of-tables)
2552 ("Table of contents" . nil)
2554 (action . (lambda (x)
2555 (switch-to-buffer ,cb)
2558 ((name . "Export functions")
2559 (candidates . (("Extract cited entries" . org-ref-extract-bibtex-entries)
2560 ("Export to html and open" . (lambda () (org-open-file (org-html-export-to-html))))
2561 ("Export to pdf and open" . (lambda ()
2562 (org-open-file (org-latex-export-to-pdf))))
2563 ("Export to manuscript pdf and open" . ox-manuscript-export-and-build-and-open)
2564 ("Export submission manuscript pdf and open" . ox-manuscript-build-submission-manuscript-and-open)
2567 (action . (lambda (x)
2568 (switch-to-buffer ,cb)
2571 ;; ** Find non-ascii charaters
2572 (defun org-ref-find-non-ascii-characters ()
2573 "Find non-ascii characters in the buffer. Useful for cleaning up bibtex files."
2575 (occur "[^[:ascii:]]"))
2577 ;; ** Sort fields in a bibtex entry
2579 (defun org-ref-sort-bibtex-entry ()
2580 "Sort fields of entry in standard order and downcase them."
2582 (bibtex-beginning-of-entry)
2583 (let* ((master '("author" "title" "journal" "volume" "number" "pages" "year" "doi" "url"))
2584 (entry (bibtex-parse-entry))
2587 (type (cdr (assoc "=type=" entry)))
2588 (key (cdr (assoc "=key=" entry))))
2590 ;; these are the fields we want to order that are in this entry
2591 (setq entry-fields (mapcar (lambda (x) (car x)) entry))
2592 ;; we do not want to reenter these fields
2593 (setq entry-fields (remove "=key=" entry-fields))
2594 (setq entry-fields (remove "=type=" entry-fields))
2596 ;;these are the other fields in the entry
2597 (setq other-fields (remove-if-not (lambda(x) (not (member x master))) entry-fields))
2600 ;; right now we only resort articles
2601 ((string= (downcase type) "article")
2604 (concat "@article{" key ",\n"
2607 (when (member field entry-fields)
2608 (format "%s = %s," (downcase field) (cdr (assoc field entry))))) master "\n")
2611 (format "%s = %s," (downcase field) (cdr (assoc field entry)))) other-fields "\n")
2613 (bibtex-find-entry key)
2615 (bibtex-clean-entry)
2618 ;; ** Clean a bibtex entry
2619 (defun org-ref-clean-bibtex-entry(&optional keep-key)
2620 "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"
2622 (bibtex-beginning-of-entry)
2624 ;; some entries do not have a key or comma in first line. We check and add it, if needed.
2625 (unless (string-match ",$" (thing-at-point 'line))
2629 ;; check for empty pages, and put eid or article id in its place
2630 (let ((entry (bibtex-parse-entry))
2631 (pages (bibtex-autokey-get-field "pages"))
2632 (year (bibtex-autokey-get-field "year"))
2633 (doi (bibtex-autokey-get-field "doi"))
2634 ;; The Journal of Chemical Physics uses eid
2635 (eid (bibtex-autokey-get-field "eid")))
2637 ;; replace http://dx.doi.org/ in doi. some journals put that in,
2638 ;; but we only want the doi.
2639 (when (string-match "^http://dx.doi.org/" doi)
2640 (bibtex-beginning-of-entry)
2641 (goto-char (car (cdr (bibtex-search-forward-field "doi" t))))
2643 (bibtex-make-field "doi")
2645 (insert (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))
2647 ;; asap articles often set year to 0, which messes up key
2648 ;; generation. fix that.
2649 (when (string= "0" year)
2650 (bibtex-beginning-of-entry)
2651 (goto-char (car (cdr (bibtex-search-forward-field "year" t))))
2653 (bibtex-make-field "year")
2655 (insert (read-string "Enter year: ")))
2657 ;; fix pages if they are empty if there is an eid to put there.
2658 (when (string= "-" pages)
2660 (bibtex-beginning-of-entry)
2661 ;; this seems like a clunky way to set the pages field.But I
2662 ;; cannot find a better way.
2663 (goto-char (car (cdr (bibtex-search-forward-field "pages" t))))
2665 (bibtex-make-field "pages")
2669 ;; replace naked & with \&
2671 (bibtex-narrow-to-entry)
2672 (bibtex-beginning-of-entry)
2673 (message "checking &")
2674 (replace-regexp " & " " \\\\& ")
2677 ;; generate a key, and if it duplicates an existing key, edit it.
2679 (let ((key (bibtex-generate-autokey)))
2681 ;; first we delete the existing key
2682 (bibtex-beginning-of-entry)
2683 (re-search-forward bibtex-entry-maybe-empty-head)
2684 (if (match-beginning bibtex-key-in-head)
2685 (delete-region (match-beginning bibtex-key-in-head)
2686 (match-end bibtex-key-in-head)))
2687 ;; check if the key is in the buffer
2688 (when (save-excursion
2689 (bibtex-search-entry key))
2691 (bibtex-search-entry key)
2692 (bibtex-copy-entry-as-kill)
2693 (switch-to-buffer-other-window "*duplicate entry*")
2695 (setq key (bibtex-read-key "Duplicate Key found, edit: " key)))
2698 (kill-new key))) ;; save key for pasting
2700 ;; run hooks. each of these operates on the entry with no arguments.
2701 ;; this did not work like i thought, it gives a symbolp error.
2702 ;; (run-hooks org-ref-clean-bibtex-entry-hook)
2707 org-ref-clean-bibtex-entry-hook)
2709 ;; sort fields within entry
2710 (org-ref-sort-bibtex-entry)
2711 ;; check for non-ascii characters
2712 (occur "[^[:ascii:]]")
2715 (defun org-ref-get-citation-year (key)
2716 "Get the year of an entry with KEY. Return year as a string."
2717 (let* ((results (org-ref-get-bibtex-key-and-file key))
2718 (bibfile (cdr results)))
2720 (insert-file-contents bibfile)
2721 (bibtex-search-entry key nil 0)
2722 (prog1 (reftex-get-bib-field "year" (bibtex-parse-entry t))
2725 ;; ** Sort cite in cite link
2726 (defun org-ref-sort-citation-link ()
2727 "Replace link at point with sorted link by year."
2729 (let* ((object (org-element-context))
2730 (type (org-element-property :type object))
2731 (begin (org-element-property :begin object))
2732 (end (org-element-property :end object))
2733 (link-string (org-element-property :path object))
2735 (setq keys (org-ref-split-and-strip-string link-string))
2736 (setq years (mapcar 'org-ref-get-citation-year keys))
2737 (setq data (mapcar* (lambda (a b) `(,a . ,b)) years keys))
2738 (setq data (cl-sort data (lambda (x y) (< (string-to-int (car x)) (string-to-int (car y))))))
2739 ;; now get the keys separated by commas
2740 (setq keys (mapconcat (lambda (x) (cdr x)) data ","))
2741 ;; and replace the link with the sorted keys
2742 (cl--set-buffer-substring begin end (concat type ":" keys))))
2744 ;; ** Shift-arrow sorting of keys in a cite link
2746 (defun org-ref-swap-keys (i j keys)
2747 "Swap the KEYS in a list with index I and J."
2748 (let ((tempi (nth i keys)))
2749 (setf (nth i keys) (nth j keys))
2750 (setf (nth j keys) tempi))
2754 (defun org-ref-swap-citation-link (direction)
2755 "Move citation at point in DIRECTION +1 is to the right, -1 to the left."
2757 (let* ((object (org-element-context))
2758 (type (org-element-property :type object))
2759 (begin (org-element-property :begin object))
2760 (end (org-element-property :end object))
2761 (link-string (org-element-property :path object))
2763 ;; We only want this to work on citation links
2764 (when (-contains? org-ref-cite-types type)
2765 (setq key (org-ref-get-bibtex-key-under-cursor))
2766 (setq keys (org-ref-split-and-strip-string link-string))
2767 (setq i (index key keys)) ;; defined in org-ref
2768 (if (> direction 0) ;; shift right
2769 (org-ref-swap-keys i (+ i 1) keys)
2770 (org-ref-swap-keys i (- i 1) keys))
2771 (setq keys (mapconcat 'identity keys ","))
2772 ;; and replace the link with the sorted keys
2773 (cl--set-buffer-substring
2777 ;; It seems the space at the end can get consumed, so we see if there
2778 ;; is a space, and add it if so. Sometimes there is a comma or period,
2779 ;; then we do not want a space.
2783 (looking-back " ")) " ")))
2784 ;; now go forward to key so we can move with the key
2785 (re-search-forward key)
2786 (goto-char (match-beginning 0)))))
2788 ;; add hooks to make it work
2789 (add-hook 'org-shiftright-hook (lambda () (org-ref-swap-citation-link 1)))
2790 (add-hook 'org-shiftleft-hook (lambda () (org-ref-swap-citation-link -1)))
2792 ;; ** context around org-ref links
2793 (defun org-ref-get-label-context (label)
2794 "Return a string of context around a LABEL."
2797 (goto-char (point-min))
2798 (when (re-search-forward
2799 (format "label:%s\\b" label) nil t)
2800 (throw 'result (buffer-substring
2809 (goto-char (point-min))
2810 (when (re-search-forward
2811 (format "\\label{%s}" label) nil t)
2812 (throw 'result (buffer-substring
2821 (goto-char (point-min))
2822 (when (re-search-forward
2823 (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t)
2824 (throw 'result (buffer-substring
2833 (goto-char (point-min))
2834 (when (re-search-forward
2835 (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t)
2836 (throw 'result (buffer-substring
2844 (throw 'result "!!! NO CONTEXT FOUND !!!"))))
2847 (defun org-ref-link-message ()
2848 "Print a minibuffer message about the link that point is on."
2852 (when (eq major-mode 'org-mode)
2853 (let* ((object (org-element-context))
2854 (type (org-element-property :type object)))
2858 ((-contains? org-ref-cite-types type)
2859 (message (org-ref-get-citation-string-at-point)))
2861 ;; message some context about the label we are referring to
2862 ((string= type "ref")
2863 (message "%scount: %s"
2864 (org-ref-get-label-context
2865 (org-element-property :path object))
2866 (org-ref-count-labels
2867 (org-element-property :path object))))
2869 ((string= type "eqref")
2870 (message "%scount: %s"
2871 (org-ref-get-label-context
2872 (org-element-property :path object))
2873 (org-ref-count-labels
2874 (org-element-property :path object))))
2876 ;; message the count
2877 ((string= type "label")
2878 (let ((count (org-ref-count-labels
2879 (org-element-property :path object))))
2880 ;; get plurality on occurrence correct
2882 (number-to-string count)
2884 (when (or (= count 0)
2888 ((string= type "custom-id")
2890 (org-open-link-from-string
2891 (format "[[#%s]]" (org-element-property :path object)))
2892 (message "%s" (org-get-heading))))
2894 ;; check if the bibliography files exist.
2895 ((string= type "bibliography")
2897 ;; object is the link you clicked on
2898 (object (org-element-context))
2899 (link-string (org-element-property :path object))
2900 (link-string-beginning)
2903 (goto-char (org-element-property :begin object))
2904 (search-forward link-string nil nil 1)
2905 (setq link-string-beginning (match-beginning 0))
2906 (setq link-string-end (match-end 0)))
2908 ;; make sure we are in link and not before the :
2909 (when (> link-string-beginning (point))
2910 (goto-char link-string-beginning))
2912 ;; now if we have comma separated bibliographies
2913 ;; we find the one clicked on. we want to
2914 ;; search forward to next comma from point
2916 (if (search-forward "," link-string-end 1 1)
2917 (setq key-end (- (match-end 0) 1)) ; we found a match
2918 (setq key-end (point)))) ; no comma found so take the point
2920 ;; and backward to previous comma from point
2922 (if (search-backward "," link-string-beginning 1 1)
2923 (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
2924 (setq key-beginning (point)))) ; no match found
2925 ;; save the key we clicked on.
2927 (org-ref-strip-string
2928 (buffer-substring key-beginning key-end)))
2929 (if (file-exists-p bibfile)
2930 (message "%s exists." bibfile)
2931 (message "!!! %s NOT FOUND !!!" bibfile))))))))))
2934 (defalias 'oro 'org-ref-open-citation-at-point)
2935 (defalias 'orc 'org-ref-citation-at-point)
2936 (defalias 'orp 'org-ref-open-pdf-at-point)
2937 (defalias 'oru 'org-ref-open-url-at-point)
2938 (defalias 'orn 'org-ref-open-notes-at-point)
2939 (defalias 'ornr 'org-ref-open-notes-from-reftex)
2941 (defalias 'orib 'org-ref-insert-bibliography-link)
2942 (defalias 'oric 'org-ref-insert-cite-link)
2943 (defalias 'orir 'org-ref-insert-ref-link)
2944 (defalias 'orsl 'org-ref-store-bibtex-entry-link)
2946 (defalias 'orcb 'org-ref-clean-bibtex-entry)
2948 ;; * Helm bibtex setup
2950 (setq helm-bibtex-additional-search-fields '(keywords))
2952 (defun helm-bibtex-candidates-formatter (candidates source)
2953 "Formats BibTeX entries for display in results list.
2954 Argument CANDIDATES helm candidates.
2955 Argument SOURCE the helm source."
2957 with width = (with-helm-window (helm-bibtex-window-width))
2958 for entry in candidates
2959 for entry = (cdr entry)
2960 for entry-key = (helm-bibtex-get-value "=key=" entry)
2961 if (assoc-string "author" entry 'case-fold)
2962 for fields = '("author" "title" "year" "=has-pdf=" "=has-note=" "=type=")
2964 for fields = '("editor" "title" "year" "=has-pdf=" "=has-note=" "=type=")
2965 for fields = (--map (helm-bibtex-clean-string
2966 (helm-bibtex-get-value it entry " "))
2968 for fields = (-update-at 0 'helm-bibtex-shorten-authors fields)
2969 for fields = (append fields
2970 (list (or (helm-bibtex-get-value "keywords" entry)
2973 (cons (s-format "$0 $1 $2 $3 $4$5 $6" 'elt
2974 (-zip-with (lambda (f w) (truncate-string-to-width f w 0 ?\s))
2975 fields (list 36 (- width 85) 4 1 1 7 7)))
2978 ;; * org-ref bibtex keywords
2979 ;; adapted from bibtex-utils.el
2980 ;; these are candidates for selecting keywords/tags
2981 (defun org-ref-bibtex-keywords ()
2982 "Get keywords defined in current bibtex file.
2983 These are in the keywords field, and are comma or semicolon separated."
2985 (goto-char (point-min))
2986 (let (keywords kstring)
2987 (while (re-search-forward "^\\s-*keywords.*{\\([^}]+\\)}" nil t)
2988 ;; TWS - remove newlines/multiple spaces:
2989 (setq kstring (replace-regexp-in-string "[ \t\n]+" " " (match-string 1)))
2992 (add-to-list 'keywords v t))
2993 (split-string kstring "\\(,\\|;\\)[ \n]*\\|{\\|}" t)))
2997 (defun org-ref-set-bibtex-keywords (keywords &optional arg)
2998 "Add KEYWORDS to a bibtex entry.
2999 If KEYWORDS is a list, it is converted to a comma-separated
3000 string. The KEYWORDS are added to the beginning of the
3001 field. Otherwise KEYWORDS should be a string of comma-separate
3002 keywords. Optional argument ARG prefix arg to replace keywords."
3003 (interactive "sKeywords: \nP")
3008 (if (listp keywords)
3009 (mapconcat 'identity keywords ", ")
3011 ;; else concatentate
3013 (if (listp keywords)
3014 (mapconcat 'identity keywords ", ")
3016 (when (not (string= "" (bibtex-autokey-get-field "keywords")))
3017 (concat ", " (bibtex-autokey-get-field "keywords"))))))
3021 (defun helm-tag-bibtex-entry ()
3022 "Helm interface to add keywords to a bibtex entry.
3023 Run this with the point in a bibtex entry."
3025 (let ((keyword-source `((name . "Existing keywords")
3026 (candidates . ,(org-ref-bibtex-keywords))
3027 (action . (lambda (candidate)
3028 (org-ref-set-bibtex-keywords
3031 (helm-marked-candidates)
3033 (fallback-source `((name . "Add new keywords")
3035 (action . (lambda (candidate)
3036 (org-ref-set-bibtex-keywords helm-pattern)
3038 (helm :sources '(keyword-source fallback-source))))
3040 (defun helm-bibtex-show-entry (key)
3041 "Show the entry for KEY in the BibTeX file.
3042 The original function in `helm-bibtex' has a bug where it finds the
3043 first key that partially matches. This version avoids that."
3045 (dolist (bibtex-file (if (listp helm-bibtex-bibliography)
3046 helm-bibtex-bibliography
3047 (list helm-bibtex-bibliography)))
3048 (let ((buf (helm-bibtex-buffer-visiting bibtex-file))
3050 (find-file bibtex-file)
3052 (lambda (key start end)
3053 (add-to-list 'entries (cons key start))))
3054 (if (assoc key entries)
3056 (goto-char (cdr (assoc key entries)))
3061 (defun org-ref-helm-tag-entries (candidates)
3062 "Set tags on selected bibtex entries from `helm-bibtex'.
3063 User is prompted for tags. This function is called from `helm-bibtex'.
3064 Argument CANDIDATES helm candidates."
3066 (let ((keywords (read-string "Keywords (comma separated): ")))
3067 (loop for key in (helm-marked-candidates)
3069 (save-window-excursion
3070 (helm-bibtex-show-entry key)
3075 ", " (bibtex-autokey-get-field "keywords")))
3078 (setq helm-source-bibtex
3079 '((name . "BibTeX entries")
3080 (init . helm-bibtex-init)
3081 (candidates . helm-bibtex-candidates)
3082 (filtered-candidate-transformer . helm-bibtex-candidates-formatter)
3083 (action . (("Insert citation" . helm-bibtex-insert-citation)
3084 ("Show entry" . helm-bibtex-show-entry)
3085 ("Open PDF file (if present)" . helm-bibtex-open-pdf)
3086 ("Open URL or DOI in browser" . helm-bibtex-open-url-or-doi)
3087 ("Insert formatted reference" . helm-bibtex-insert-reference)
3088 ("Insert BibTeX key" . helm-bibtex-insert-key)
3089 ("Insert BibTeX entry" . helm-bibtex-insert-bibtex)
3090 ("Attach PDF to email" . helm-bibtex-add-PDF-attachment)
3091 ("Edit notes" . helm-bibtex-edit-notes)
3092 ("Add keywords to entries" . org-ref-helm-tag-entries)
3095 (defun helm-bibtex-format-org-ref (keys)
3096 "Insert selected KEYS as cite link. Append KEYS if you are on a link.
3097 Technically, this function should return a string that is inserted by helm. This function does the insertion and gives helm an empty string to insert. This lets us handle appending to a link properly.
3099 In the helm-bibtex buffer, C-u will give you a helm menu to select a new link type for the selected entries.
3101 C-u C-u will change the key at point to the selected keys."
3102 (let* ((object (org-element-context))
3103 (last-char (save-excursion
3104 (when (org-element-property :end object)
3105 (goto-char (org-element-property :end object))
3108 (if (looking-at " ")
3112 ;; case where we are in a link
3113 ((and (equal (org-element-type object) 'link)
3116 (org-element-property :type object)))
3118 ;; no prefix. append keys
3119 ((equal helm-current-prefix-arg nil)
3120 (goto-char (org-element-property :end object))
3121 (while (looking-back " ") (backward-char))
3122 (insert (concat "," (mapconcat 'identity keys ","))))
3123 ;; double prefix, replace key at point
3124 ((equal helm-current-prefix-arg '(16))
3125 (setf (buffer-substring
3126 (org-element-property :begin object)
3127 (org-element-property :end object))
3129 (replace-regexp-in-string
3130 (car (org-ref-get-bibtex-key-and-file)) ; key
3131 (mapconcat 'identity keys ",") ; new keys
3132 (org-element-property :raw-link object))
3133 ;; replace space at end to avoid collapsing into next word.
3135 ;; and we want to go to the end of the new link
3137 (org-element-property :end (org-element-context))))
3139 (message "Not found"))))
3141 ;; We are next to a link, and we want to append
3142 ;; next to a link means one character back is on a link.
3144 (unless (bobp) (backward-char))
3145 (and (equal (org-element-type (org-element-context)) 'link)
3148 (org-element-property :type (org-element-context)))))
3149 (while (looking-back " ") (backward-char))
3150 (insert (concat "," (mapconcat 'identity keys ","))))
3152 ;; insert fresh link
3154 ;;(message-box "fresh link")
3156 (concat (if (equal helm-current-prefix-arg '(4))
3157 (helm :sources `((name . "link types")
3158 (candidates . ,org-ref-cite-types)
3159 (action . (lambda (x) x))))
3160 org-ref-default-citation-link)
3162 (s-join "," keys))))))
3163 ;; return empty string for helm
3166 (setq helm-bibtex-format-citation-functions
3167 '((org-mode . helm-bibtex-format-org-ref)))
3170 (defun org-ref-helm-insert-cite-link (arg)
3171 "org-ref function to use helm-bibtex to insert a citation link.
3172 With one prefix arg, insert a ref link.
3173 With two prefix args, insert a label link."
3177 (let ((helm-bibtex-bibliography (org-ref-find-bibliography)))
3180 (org-ref-helm-insert-ref-link))
3182 (org-ref-helm-insert-label-link))))
3185 ;; add our own fallback entries where we want them. These appear in reverse order of adding in the menu
3186 (setq helm-bibtex-fallback-options
3187 (-insert-at 1 '("Crossref" . "http://search.crossref.org/?q=%s") helm-bibtex-fallback-options))
3189 (setq helm-bibtex-fallback-options
3192 '("Scopus" . "http://www.scopus.com/scopus/search/submit/xadvanced.url?searchfield=TITLE-ABS-KEY(%s)")
3193 helm-bibtex-fallback-options))
3195 (setq helm-bibtex-fallback-options
3196 (-insert-at 1 '("WOS" . "http://gateway.webofknowledge.com/gateway/Gateway.cgi?topic=%s&GWVersion=2&SrcApp=WEB&SrcAuth=HSB&DestApp=UA&DestLinkType=GeneralSearchSummary") helm-bibtex-fallback-options))
3198 (defun org-ref-get-citation-string-at-point ()
3199 "Get a string of a formatted citation."
3200 (let* ((results (org-ref-get-bibtex-key-and-file))
3202 (bibfile (cdr results)))
3206 (insert-file-contents bibfile)
3207 (bibtex-search-entry key)
3208 (org-ref-bib-citation)))
3209 "!!! No entry found !!!" )))
3212 (defun org-ref-cite-candidates ()
3213 "Generate the list of possible candidates for click actions on a cite link.
3214 Checks for pdf and doi, and add appropriate functions."
3215 (let* ((results (org-ref-get-bibtex-key-and-file))
3217 (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
3218 (bibfile (cdr results))
3219 (url (save-excursion
3221 (insert-file-contents bibfile)
3222 (bibtex-search-entry key)
3223 (bibtex-autokey-get-field "url"))))
3224 (doi (save-excursion
3226 (insert-file-contents bibfile)
3227 (bibtex-search-entry key)
3228 ;; I like this better than bibtex-url which does not always find
3230 (bibtex-autokey-get-field "doi"))))
3231 (candidates `(("Quit" . org-ref-citation-at-point)
3232 ("Open bibtex entry" . org-ref-open-citation-at-point))))
3233 ;; for some reason, when there is no doi or url, they are returned as "". I
3234 ;; prefer nil so we correct this here.
3235 (when (string= doi "") (setq doi nil))
3236 (when (string= url "") (setq url nil))
3238 ;; Conditional pdf functions
3239 (if (file-exists-p pdf-file)
3242 '("Open pdf" . org-ref-open-pdf-at-point)
3246 '("Try to get pdf" . (lambda ()
3247 (save-window-excursion
3248 (org-ref-open-citation-at-point)
3249 (bibtex-beginning-of-entry)
3250 (doi-utils-get-bibtex-entry-pdf))))
3256 '("Open notes" . org-ref-open-notes-at-point)
3259 ;; conditional url and doi functions
3263 '("Open in browser" . org-ref-open-url-at-point)
3268 (add-to-list 'candidates x t))
3269 `(("WOS" . org-ref-wos-at-point)
3270 ("Related articles in WOS" . org-ref-wos-related-at-point)
3271 ("Citing articles in WOS" . org-ref-wos-citing-at-point)
3272 ("Google Scholar" . org-ref-google-scholar-at-point)
3273 ("Pubmed" . org-ref-pubmed-at-point)
3274 ("Crossref" . org-ref-crossref-at-point)
3279 '("Copy formatted citation to clipboard" . org-ref-copy-entry-as-summary)
3284 '("Copy key to clipboard" . (lambda ()
3286 (car (org-ref-get-bibtex-key-and-file)))))
3291 '("Copy bibtex entry to file" . org-ref-copy-entry-at-point-to-file)
3296 '("Email bibtex entry and pdf" . (lambda ()
3298 (org-ref-open-citation-at-point)
3299 (email-bibtex-entry))))
3301 ;; finally return a numbered list of the candidates
3303 for cell in candidates
3304 collect (cons (format "%2s. %s" i (car cell))
3308 (defvar org-ref-helm-user-candidates '()
3309 "List of user-defined candidates to act when clicking on a cite link.
3310 This is a list of cons cells '((\"description\" . action)). The action function should not take an argument, and should assume point is on the cite key of interest.")
3312 ;; example of adding your own function
3314 'org-ref-helm-user-candidates
3315 '("Example" . (lambda () (message-box "You did it!")))
3319 (defun org-ref-cite-click-helm (key)
3320 "Open helm for actions on a cite link.
3323 1. get name and candidates before entering helm because we need
3326 2. switch back to the org buffer before evaluating the
3327 action. most of them need the point and buffer.
3329 KEY is returned for the selected item(s) in helm."
3331 (let ((name (org-ref-get-citation-string-at-point))
3332 (candidates (org-ref-cite-candidates))
3333 (cb (current-buffer)))
3335 (helm :sources `(((name . ,name)
3336 (candidates . ,candidates)
3337 (action . (lambda (f)
3338 (switch-to-buffer cb)
3340 ((name . "User functions")
3341 (candidates . ,org-ref-helm-user-candidates)
3342 (action . (lambda (f)
3343 (switch-to-buffer cb)
3347 ;; * Hydra menus in org-ref
3349 (when (featurep 'hydra)
3351 (setq hydra-is-helpful t)
3353 (defhydra org-ref-cite-hydra (:color blue)
3355 _p_: Open pdf _w_: WOS _g_: Google Scholar _K_: Copy citation to clipboard
3356 _u_: Open url _r_: WOS related _P_: Pubmed _k_: Copy key to clipboard
3357 _n_: Open notes _c_: WOS citing _C_: Crossref _f_: Copy bibtex entry to file
3358 _o_: Open entry _e_: Email entry and pdf
3360 ("o" org-ref-open-citation-at-point nil)
3361 ("p" org-ref-open-pdf-at-point nil)
3362 ("n" org-ref-open-notes-at-point nil)
3363 ("u" org-ref-open-url-at-point nil)
3364 ("w" org-ref-wos-at-point nil)
3365 ("r" org-ref-wos-related-at-point nil)
3366 ("c" org-ref-wos-citing-at-point nil)
3367 ("g" org-ref-google-scholar-at-point nil)
3368 ("P" org-ref-pubmed-at-point nil)
3369 ("C" org-ref-crossref-at-point nil)
3370 ("K" org-ref-copy-entry-as-summary nil)
3373 (car (org-ref-get-bibtex-key-and-file)))) nil)
3374 ("f" org-ref-copy-entry-at-point-to-file nil)
3376 ("e" (save-excursion
3377 (org-ref-open-citation-at-point)
3378 (email-bibtex-entry)) nil)))
3381 (defun org-ref-help ()
3382 "Open the org-ref manual."
3384 (find-file (expand-file-name
3386 (file-name-directory
3387 (find-library-name "org-ref")))))
3390 (defun org-ref-org-menu ()
3391 "Add org-ref menu to the Org menu."
3395 '( ["Insert citation" org-ref-helm-insert-cite-link]
3396 ["Insert ref" org-ref-helm-insert-ref-link]
3397 ["Insert label" org-ref-helm-insert-label-link]
3399 ["List of figures" org-ref-list-of-figures]
3400 ["List of tables" org-ref-list-of-tables]
3401 ["Extract bibtex entries" org-ref-extract-bibtex-entries]
3402 ["Check org-file" org-ref]
3404 ["Help" org-ref-help]
3405 ["Customize org-ref" (customize-group 'org-ref)])
3408 (easy-menu-change '("Org") "--" nil "Show/Hide"))
3410 (add-hook 'org-mode-hook 'org-ref-org-menu)
3415 ;;; org-ref.el ends here
projects / org-ref.git / blob