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org-ref-core.el
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;;; org-ref-core.el --- citations, cross-references and bibliographies in org-mode
;; Copyright(C) 2014-2017 John Kitchin
;; This file is not currently part of GNU Emacs.
;; This program is free software; you can redistribute it and/or
;; modify it under the terms of the GNU General Public License as
;; published by the Free Software Foundation; either version 2, or (at
;; your option) any later version.
;; This program is distributed in the hope that it will be useful, but
;; WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;; General Public License for more details.
;; You should have received a copy of the GNU General Public License
;; along with this program ; see the file COPYING. If not, write to
;; the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
;; Boston, MA 02111-1307, USA.
;;; Commentary:
;;
;; Lisp code to setup bibliography, cite, ref and label org-mode links.
;; Also sets up reftex and helm for org-mode citations. The links are
;; clickable and do things that are useful. You should really read
;; org-ref.org in this package for details.
;;
;;; Code:
(eval-when-compile
(require 'cl-lib))
(require 'dash)
(require 'f)
(require 'htmlize)
(require 's)
(require 'doi-utils)
(add-to-list 'load-path
(expand-file-name
"citeproc"
(file-name-directory (or load-file-name (buffer-file-name)))))
(add-to-list 'load-path
(expand-file-name
"citeproc/csl"
(file-name-directory (or load-file-name (buffer-file-name)))))
(require 'org-ref-bibtex)
(require 'org-ref-utils)
(require 'org-ref-glossary)
(require 'org)
(require 'org-element)
(require 'ox)
(require 'parsebib)
(require 'reftex-cite)
(defvar org-export-exclude-tags)
(defvar warning-suppress-types)
(declare-function bibtex-completion-get-entry "bibtex-completion")
(declare-function bibtex-completion-edit-notes "bibtex-completion")
;;* Custom variables
(defgroup org-ref nil
"Customization group for org-ref."
:tag "Org Ref"
:group 'org)
(defcustom org-ref-bibliography-notes
nil
"Filename where you will put all your notes about an entry in the default bibliography.
Used by backends that append all notes as entries in a single file.
See also `org-ref-notes-function'"
:type '(choice (const nil)
(file))
:group 'org-ref)
(defcustom org-ref-notes-directory
nil
"Directory where you will put all your notes about an entry in the default bibliography.
Used for backends that create a single file of notes per entry.
See also `org-ref-notes-function'."
:type 'directory
:group 'org-ref)
(defcustom org-ref-default-bibliography
nil
"List of bibtex files to search for.
You should use full-paths for each file. Note that you must
include a bibliography link in your document if you will be
exporting it to pdf; org-ref-default-bibliography is not
used by the LaTeX exporter."
:type '(repeat :tag "List of bibtex files" file)
:group 'org-ref)
(defcustom org-ref-pdf-directory
nil
"Directory where pdfs are stored by key.
Put a trailing / in the name."
:type '(choice directory (repeat directory))
:group 'org-ref)
(defcustom org-ref-default-citation-link
"cite"
"The default type of citation link to use."
:type 'string
:group 'org-ref)
(defcustom org-ref-insert-cite-key
"C-c ]"
"Keyboard shortcut to insert a citation."
:type 'string
:group 'org-ref)
(defcustom org-ref-completion-library
'org-ref-helm-bibtex
"Symbol for library to define completion functions.
The completion library should provide functions for
`org-ref-insert-link-function', `org-ref-insert-cite-function',
`org-ref-insert-label-function', `org-ref-insert-ref-function',
and `org-ref-cite-onclick-function', and set those variables to
the values of those functions."
:type 'symbol
:options '(org-ref-helm-bibtex ; completion with helm + helm-bibtex
org-ref-helm-cite ; completion with helm in org-ref
org-ref-ivy-cite ; completion with ivy
org-ref-reftex ; org-completion
)
:group 'org-ref)
(defcustom org-ref-insert-link-function
nil
"Generic function for inserting org-ref links.
The function should take a prefix arg.
No arg means insert a cite link
1 arg means insert a ref link
2 args means insert a label."
:type 'function
:group 'org-ref)
(defcustom org-ref-insert-cite-function
nil
"Function to call to insert citation links.
This function should prompt for keys with completion, and insert
the citation link into the buffer."
:type 'function
:group 'org-ref)
(defcustom org-ref-prefer-bracket-links nil
"If non-nil use bracketed links when inserting them."
:type 'boolean
:group 'org-ref)
(defcustom org-ref-cite-completion-function
nil
"Function to prompt for keys with completion."
:type '(choice (const nil)
(function))
:group 'org-ref)
(defcustom org-ref-insert-label-function
nil
"Function to call to insert label links.
This function should prompt for a label, and insert the label
link."
:type 'function
:group 'org-ref)
(defcustom org-ref-insert-ref-function
nil
"Function to call to insert ref links.
This function should prompt for a label with completion, and
insert the ref link."
:type 'function
:group 'org-ref)
(defcustom org-ref-cite-onclick-function
nil
"Function that runs when you click on a cite link.
The function must take one argument which is the path of the link
that was clicked on. This function is normally set by the
function in `org-ref-completion-library'."
:type 'function
:group 'org-ref)
;; define key for inserting citations
(define-key org-mode-map
(kbd org-ref-insert-cite-key)
org-ref-insert-link-function)
(defcustom org-ref-cite-keymap
(let ((map (copy-keymap org-mouse-map)))
(define-key map (kbd "H-o") 'org-ref-cite-hydra/body)
(define-key map (kbd "H-b") 'org-ref-open-citation-at-point)
(define-key map (kbd "H-u") 'org-ref-open-url-at-point)
(define-key map (kbd "H-p") 'org-ref-open-pdf-at-point)
(define-key map (kbd "H-n") 'org-ref-open-notes-at-point)
(define-key map (kbd "H-r") 'org-ref-wos-related-at-point)
(define-key map (kbd "H-c") 'org-ref-wos-citing-at-point)
(define-key map (kbd "H-e") (lambda ()
"Email entry at point"
(interactive)
(org-ref-open-citation-at-point)
(org-ref-email-bibtex-entry)))
(define-key map (kbd "H-g") 'org-ref-google-scholar-at-point)
(define-key map (kbd "H-f") (lambda ()
(interactive)
(save-excursion
(org-ref-open-citation-at-point)
(kill-new
(org-ref-format-bibtex-entry-at-point)))))
(define-key map (kbd "H-w") (lambda ()
(interactive)
(kill-new (car (org-ref-get-bibtex-key-and-file)))))
(define-key map (kbd "H-W") (lambda ()
"Copy all the keys at point."
(interactive)
(kill-new (org-element-property :path (org-element-context)))))
(define-key map (kbd "H-y") (lambda ()
"Paste key at point. Assumes the first thing in the killring is a key."
(interactive)
(org-ref-insert-key-at-point (car kill-ring))))
;; Navigation keys
(define-key map (kbd "C-<left>") 'org-ref-previous-key)
(define-key map (kbd "C-<right>") 'org-ref-next-key)
;; rearrangement keys
(define-key map (kbd "S-<left>") (lambda () (interactive) (org-ref-swap-citation-link -1)))
(define-key map (kbd "S-<right>") (lambda () (interactive) (org-ref-swap-citation-link 1)))
(define-key map (kbd "S-<up>") 'org-ref-sort-citation-link)
(define-key map (kbd "<tab>") (lambda () (interactive)
(funcall org-ref-insert-cite-function)))
map)
"Keymap for cite links."
:type 'symbol
:group 'org-ref)
(defcustom org-ref-bibliography-entry-format
'(("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>.")
("book" . "%a, %t, %u (%y).")
("techreport" . "%a, %t, %i, %u (%y).")
("proceedings" . "%e, %t in %S, %u (%y).")
("inproceedings" . "%a, %t, %p, in %b, edited by %e, %u (%y)"))
"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."
:type '(alist :key-type (string) :value-type (string))
:group 'org-ref)
(defcustom org-ref-note-title-format
"** TODO %y - %t
:PROPERTIES:
:Custom_ID: %k
:AUTHOR: %9a
:JOURNAL: %j
:YEAR: %y
:VOLUME: %v
:PAGES: %p
:DOI: %D
:URL: %U
:END:
"
"String to format the title and properties drawer of a note.
See the `org-ref-reftex-format-citation' docstring for the escape
codes."
:type 'string
:group 'org-ref)
(defcustom org-ref-ref-html "<a class='org-ref-reference' href=\"#%s\">%s</a>"
"HTML code to represent a reference."
:type 'string
:group 'org-ref)
(defcustom org-ref-notes-function #'org-ref-notes-function-one-file
"Function to open the notes for the bibtex key in a cite link at point.
The default behavior adds entries to a long file with headlines
for each entry. It also tries to be compatible with `org-bibtex'.
An alternative is `org-ref-notes-function-many-files'. Use that
if you prefer the `bibtex-completion' approach, which also
supports an additional method for storing notes. See
`bibtex-completion-notes-path' for more information. You may also
want to set `org-ref-notes-directory'."
:type 'function
:group 'org-ref)
(defcustom org-ref-open-notes-function
(lambda ()
(org-show-entry)
(outline-show-branches)
(outline-show-children)
(org-cycle '(64))
(recenter-top-bottom 0))
"User-defined way to open a notes entry.
This is executed after the entry is found in
`org-ref-open-bibtex-notes', 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."
:type 'function
:group 'org-ref)
(defcustom org-ref-create-notes-hook
'((lambda ()
(org-narrow-to-subtree)
(insert (format "cite:%s\n" (org-entry-get (point) "Custom_ID")))))
"List of hook functions to run in the note entry after it is created.
The function takes no arguments. It could be used to insert links
to the citation, or pdf, etc..."
:type 'hook
:group 'org-ref)
(defcustom org-ref-open-pdf-function
'org-ref-open-pdf-at-point
"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'."
:type 'function
:group 'org-ref)
(defcustom org-ref-get-pdf-filename-function
'org-ref-get-pdf-filename
"User-defined function to get a filename from a bibtex key.
The function must take a key as an argument, and return the path
to the corresponding filename. The default is
`org-ref-get-pdf-filename'. Alternative values are
`org-ref-get-mendeley-filename' or
`org-ref-get-pdf-filename-helm-bibtex'."
:type 'function
:group 'org-ref)
(defcustom org-ref-clean-bibtex-key-function
(lambda (key)
(replace-regexp-in-string ":" "" key))
"Function to modify a bibtex key.
The default behavior is to remove : from the key."
:type 'function
:group 'org-ref)
(defcustom org-ref-show-citation-on-enter t
"If non-nil show the citation summary.
Uses a hook function to display the message in the minibuffer."
:type 'boolean
:group 'org-ref)
(defcustom org-ref-natbib-types
'("citet" "citet*" "citep" "citep*"
"citealt" "citealt*" "citealp" "citealp*"
"citenum" "citetext"
"citeauthor" "citeauthor*"
"citeyear" "citeyear*" "citeyearpar"
"Citet" "Citep" "Citealt" "Citealp" "Citeauthor")
"natbib cite commands, http://tug.ctan.org/macros/latex/contrib/natbib/natnotes.pdf"
:type '(repeat :tag "List of citation types" string)
:group 'org-ref)
(defcustom org-ref-biblatex-types
'("Cite"
"parencite" "Parencite"
"footcite" "footcitetext"
"textcite" "Textcite"
"smartcite" "Smartcite"
"cite*" "parencite*" "supercite"
"autocite" "Autocite" "autocite*" "Autocite*"
"Citeauthor*"
"citetitle" "citetitle*"
"citedate" "citedate*"
"citeurl"
"fullcite" "footfullcite"
;; "volcite" "Volcite" cannot support the syntax
"notecite" "Notecite"
"pnotecite" "Pnotecite"
"fnotecite"
;; multicites. Very limited support for these.
"cites" "Cites" "parencites" "Parencites"
"footcites" "footcitetexts"
"smartcites" "Smartcites" "textcites" "Textcites"
"supercites" "autocites" "Autocites")
"biblatex commands
http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf"
:type '(repeat :tag "List of citation types" string)
:group 'org-ref)
(defcustom org-ref-cite-types
(append
'("cite" "nocite") ;; the default latex cite commands
org-ref-natbib-types
org-ref-biblatex-types
;; for the bibentry package
'("bibentry"))
"List of citation types known in `org-ref'."
:type '(repeat :tag "List of citation types" string)
:group 'org-ref)
(defcustom org-ref-ref-types
'("ref" "eqref" "pageref" "nameref" "autoref" "cref" "Cref")
"List of ref link types."
:type '(repeat :tag "List of ref types" string)
:group 'org-ref)
(defcustom org-ref-default-ref-type "ref"
"Default ref link type to use when inserting ref links"
:type 'string
:group 'org-ref)
(defcustom org-ref-clean-bibtex-entry-hook
'(org-ref-bibtex-format-url-if-doi
orcb-key-comma
org-ref-replace-nonascii
orcb-&
orcb-%
org-ref-title-case-article
orcb-clean-year
orcb-key
orcb-clean-doi
orcb-clean-pages
orcb-check-journal
org-ref-sort-bibtex-entry
orcb-fix-spacing)
"Hook that is run in `org-ref-clean-bibtex-entry'.
The functions should have no arguments, and
operate on the bibtex entry at point. You can assume point starts
at the beginning of the entry. These functions are wrapped in
`save-restriction' and `save-excursion' so you do not need to
save the point position.
Org ref contains some functions that are not included by default
such as `orcb-clean-nil' or `orcb-clean-nil-opinionated' that
users may be interested in adding themselves."
:group 'org-ref
:type 'hook)
(defcustom org-ref-bibtex-sort-order
'(("article" . ("author" "title" "journal" "volume" "number" "pages" "year" "doi" "url"))
("inproceedings" . ("author" "title" "booktitle" "year" "volume" "number" "pages" "doi" "url"))
("book" . ("author" "title" "year" "publisher" "url")))
"A-list of bibtex entry fields and the order to sort an entry with.
\(entry-type . (list of fields). This is used in
`org-ref-sort-bibtex-entry'. Entry types not listed here will
have fields sorted alphabetically."
:type '(alist :key-type (string) :value-type (repeat string))
:group 'org-ref)
(defcustom org-ref-printbibliography-cmd "\\printbibliography"
"LaTeX command to print bibliography. Customize this to add options."
:type 'string
:group 'org-ref)
(defvar org-ref-bibliography-files
nil
"Variable to hold bibliography files to be searched.")
(defcustom org-ref-show-broken-links t
"If non-nil show bad org-ref links in a warning face."
:type 'boolean
:group 'org-ref)
(defcustom org-ref-enable-colon-insert nil
"If non-nil enable colon to insert cites, labels, and ref links."
:type 'booleanp
:group 'org-ref)
(defcustom org-ref-label-use-font-lock t
"If non-nil use font-lock to find labels in the buffer.
If nil, each time you ask for labels the whole buffer will be
searched, which may be slower.")
(defun org-ref-colon-insert-link (arg)
"Function to run when : has a special meaning.
See `org-ref-enable-colon-insert'."
(interactive "P")
(insert ":")
(cond
;; cite links
((save-excursion
(backward-word 1)
(looking-at (regexp-opt org-ref-cite-types)))
(funcall org-ref-insert-cite-function))
((save-excursion
(backward-word 1)
(looking-at "label:"))
(funcall org-ref-insert-label-function))
((save-excursion
(backward-word 1)
(looking-at (regexp-opt org-ref-ref-types)))
(funcall org-ref-insert-ref-function))))
(when org-ref-enable-colon-insert
(define-key org-mode-map ":"
'(menu-item "maybe-cite" nil
:filter (lambda (&optional _)
(unless (org-in-src-block-p)
#'org-ref-colon-insert-link)))))
(defun org-ref-change-cite-type (new-type)
"Change the cite type to NEW-TYPE."
(interactive (list (completing-read "Type: " org-ref-cite-types)))
(let* ((cite-link (org-element-context))
(old-type (org-element-property :type cite-link))
(begin (org-element-property :begin cite-link))
(end (org-element-property :end cite-link))
(bracketp (eq 'bracket (org-element-property :format cite-link)))
(path (org-element-property :path cite-link))
(deltap (- (point) begin)))
;; note this does not respect brackets
(setf (buffer-substring begin end)
(concat
(if bracketp "[[" "")
new-type ":" path
(if bracketp "]]" "")))
;; try to preserve the character the point is on.
(goto-char (+ begin deltap (- (length new-type) (length old-type))))))
(defun org-ref-change-ref-type (new-type)
"Change the ref type to NEW-TYPE."
(interactive (list (completing-read "Type: " org-ref-ref-types)))
(let* ((cite-link (org-element-context))
(old-type (org-element-property :type cite-link))
(begin (org-element-property :begin cite-link))
(end (org-element-property :end cite-link))
(bracketp (eq 'bracket (org-element-property :format cite-link)))
(path (org-element-property :path cite-link))
(deltap (- (point) begin)))
;; note this does not respect brackets
(setf (buffer-substring begin end)
(concat
(if bracketp "[[" "")
new-type ":" path
(if bracketp "]]" "")))
;; try to preserve the character the point is on.
(goto-char (+ begin deltap (- (length new-type) (length old-type))))))
;;* Messages for link at cursor
(defvar org-ref-message-timer nil
"Variable to store the link message timer in.")
;;;###autoload
(defun org-ref-show-link-messages ()
"Turn on link messages.
You will see a message in the minibuffer when on a cite, ref or
label link."
(interactive)
(or org-ref-message-timer
(setq org-ref-message-timer
(run-with-idle-timer 0.5 t 'org-ref-link-message)
org-ref-show-citation-on-enter t)))
;;;###autoload
(defun org-ref-cancel-link-messages ()
"Stop showing messages in minibuffer when on a link."
(interactive)
(cancel-timer org-ref-message-timer)
(setq org-ref-message-timer nil
org-ref-show-citation-on-enter nil))
(when org-ref-show-citation-on-enter
(org-ref-show-link-messages))
;;;###autoload
(defun org-ref-change-completion ()
"Change the completion backend.
Options are \"org-ref-helm-bibtex\", \"org-ref-helm-cite\",
\"org-ref-ivy-cite\" and \"org-ref-reftex\"."
(interactive)
(require
(intern
(completing-read "Backend: " '("org-ref-helm-bibtex"
"org-ref-helm-cite"
"org-ref-ivy-cite"
"org-ref-reftex")
nil
t
"org-ref-helm-cite"))))
;;** Messages for context under mouse pointer
(defvar org-ref-last-mouse-pos nil
"Stores last mouse position for use in `org-ref-mouse-message'.")
(defun org-ref-can-move-p ()
"See if a character is under the mouse.
If so return the position for `goto-char'."
(let* ((line (cddr org-ref-last-mouse-pos))
(col (cadr org-ref-last-mouse-pos)))
(save-excursion
(goto-char (window-start))
(forward-line line)
(if
(> (- (line-end-position) (line-beginning-position)) col)
(progn (forward-char col) (point))
nil))))
;;;###autoload
(defun org-ref-mouse-message ()
"Display message for link under mouse cursor."
(interactive)
(when (not (equal (mouse-position) org-ref-last-mouse-pos))
(setq org-ref-last-mouse-pos (mouse-position))
(let ((p (org-ref-can-move-p)))
(when p
(save-excursion
(goto-char p)
(org-ref-link-message))))))
(defvar org-ref-message-timer-mouse nil
"Store mouse timer.")
(defvar org-ref-mouse-message-interval 0.5
"How often to run the mouse message timer in seconds.")
;;;###autoload
(defun org-ref-mouse-messages-on ()
"Turn on mouse messages."
(interactive)
(or org-ref-message-timer-mouse
(setq org-ref-message-timer-mouse
(run-at-time "0.5 sec"
org-ref-mouse-message-interval
'org-ref-mouse-message))))
;;;###autoload
(defun org-ref-mouse-messages-off ()
"Turn off mouse messages."
(interactive)
(cancel-timer org-ref-message-timer-mouse)
(setq org-ref-message-timer-mouse nil)
(message "Mouse messages are off"))
;;* font lock for org-ref
(defcustom org-ref-colorize-links
t
"When non-nil, change colors of links."
:type 'boolean
:group 'org-ref)
(defcustom org-ref-cite-color
"forest green"
"Color of cite like links."
:type 'string
:group 'org-ref)
(defcustom org-ref-ref-color
"dark red"
"Color of ref like links."
:type 'string
:group 'org-ref)
(defcustom org-ref-label-color
"dark magenta"
"Color of label links."
:type 'string
:group 'org-ref)
(defcustom org-ref-latex-bib-resolve-func #'file-relative-name
"used to expand paths to the bibliography file on latex export."
:type 'function
:group 'org-ref)
(defvar org-ref-cite-re
(concat "\\(" (mapconcat
(lambda (x)
(replace-regexp-in-string "\\*" "\\\\*" x))
org-ref-cite-types "\\|") "\\):"
"\\([a-zA-Z0-9_:\\./-]+,?\\)+")
"Regexp for cite links.
Group 1 contains the cite type.
Group 2 contains the keys.")
(defvar org-ref-label-re
"label:\\([a-zA-Z0-9_:-]+,?\\)+"
"Regexp for label links.")
(defvar org-ref-ref-re
"\\(eq\\)?ref:\\([a-zA-Z0-9_:-]+,?\\)+"
"Regexp for ref links.")
(defface org-ref-cite-face
`((t (:inherit org-link
:foreground ,org-ref-cite-color)))
"Color for cite-like links in org-ref.")
(defface org-ref-label-face
`((t (:inherit org-link :foreground ,org-ref-label-color)))
"Color for ref links in org-ref.")
(defface org-ref-ref-face
`((t (:inherit org-link :foreground ,org-ref-ref-color)))
"Face for ref links in org-ref.")
;;** Font-lock org-ref links
;; We use functions to search for the next link, and then use org-mode to find
;; the boundaries. I wasn't able to figure out robust regexps for these links
;; that includes all possible link syntaxes eg. bare, [[cite:key]] and
;; [[cite:key] [text]]. Using regexps might be a bit more efficient, so if they
;; ever get figured out, we could eliminate the org-element code in these
;; functions.
;; These functions are not used with org-9. I define them here to make
;; byte-compiling quiet.
(defun org-ref-match-next-cite-link (_) nil)
(defun org-ref-match-next-label-link (_) nil)
(defun org-ref-match-next-ref-link (_) nil)
(defun org-ref-make-org-link-cite-key-visible (_) nil)
(when (not (fboundp 'org-link-set-parameters))
(defun org-ref-match-next-cite-link (&optional limit)
"Search forward to next cite link up to LIMIT
Add a tooltip to the match."
(when (and (re-search-forward org-ref-cite-re limit t)
(not (org-in-src-block-p))
(not (org-at-comment-p)))
;; we think we are on a cite link lets get on it and make sure
(forward-char -2)
(let ((this-link (org-element-context)))
(if (-contains? org-ref-cite-types (org-element-property :type this-link))
;; we are on a cite link
(progn
(when org-ref-show-citation-on-enter
(add-text-properties
(org-element-property :begin this-link)
(- (org-element-property :end this-link)
(org-element-property :post-blank this-link))
(list
'help-echo (lambda (window object position)
(save-excursion
(goto-char position)
;; Here we wrap the citation string to a reasonable size.
(let ((s (org-ref-format-entry
(org-ref-get-bibtex-key-under-cursor))))
(with-temp-buffer
(insert s)
(fill-paragraph)
(buffer-string))))))))
(set-match-data
(list (org-element-property :begin this-link)
(- (org-element-property :end this-link)
(org-element-property :post-blank this-link))))
(goto-char (org-element-property :end this-link)))
;; Must be a false match.
;; somehow were not on a
;; cite link, so we try
;; again.
(org-ref-match-next-cite-link limit)))))
(defun org-ref-match-next-label-link (limit)
"Find next label link up to LIMIT.
Add tooltip."
(if (and (re-search-forward "label:\\([[:alnum:]]\\)\\{2,\\}" limit t)
(not (org-in-src-block-p))
(not (org-at-comment-p)))
(progn
(forward-char -2)
(let ((this-link (org-element-context)))
(if (string= "label" (org-element-property :type this-link))
;; on a label
(progn
(add-text-properties
(org-element-property :begin this-link)
(- (org-element-property :end this-link)
(org-element-property :post-blank this-link))
(list
'help-echo (lambda (window object position)
(save-excursion
(goto-char position)
(let ((s (org-ref-link-message)))
(with-temp-buffer
(insert s)
(fill-paragraph)
(buffer-string)))))))
(set-match-data
(list (org-element-property :begin this-link)
(- (org-element-property :end this-link)
(org-element-property :post-blank this-link))))
(goto-char (org-element-property :end this-link)))
;; false match
(org-ref-match-next-label-link limit))))))
(defun org-ref-match-next-ref-link (limit)
"Find next ref link up to LIMIT.
Add tooltip to the link. We avoid tags by not finding :ref: in
tags."
(when (and (re-search-forward "[^:]\\(eq\\)?ref:\\([[:alnum:]]\\)\\{2,\\}" limit t)
(not (org-in-src-block-p))
(not (org-at-comment-p)))
;; we think we are on a ref link, lets make sure.
(forward-char -2)
(let ((this-link (org-element-context)))
(if (-contains? org-ref-ref-types
(org-element-property :type this-link))
;; we are, so we do our business
(progn
(add-text-properties
(org-element-property :begin this-link)
(- (org-element-property :end this-link)
(org-element-property :post-blank this-link))
(list
'help-echo (lambda (window object position)
(save-excursion
(goto-char position)
(let ((s (org-ref-link-message)))
(with-temp-buffer
(insert s)
(fill-paragraph)
(buffer-string)))))))
(set-match-data
(list (org-element-property :begin this-link)
(- (org-element-property :end this-link)
(org-element-property :post-blank this-link))))
(goto-char (org-element-property :end this-link)))
;; False match, let's try again
(org-ref-match-next-ref-link limit)))))
(defun org-ref-match-next-bibliography-link (limit)
"Find next bibliography link up to LIMIT.
Add tooltip to the link."
(when (and (re-search-forward "bibliography:\\([[:alnum:]]\\)\\{2,\\}" limit t)
(not (org-in-src-block-p))
(not (org-at-comment-p)))
(forward-char -2)
(let ((this-link (org-element-context)))
(add-text-properties
(org-element-property :begin this-link)
(- (org-element-property :end this-link)
(org-element-property :post-blank this-link))
(list
'help-echo (lambda (window object position)
(save-excursion
(goto-char position)
(let ((s (org-ref-link-message)))
(with-temp-buffer
(insert s)
(fill-paragraph)
(buffer-string)))))))
(set-match-data
(list (org-element-property :begin this-link)
(- (org-element-property :end this-link)
(org-element-property :post-blank this-link))))
(goto-char (org-element-property :end this-link)))))
(defun org-ref-match-next-bibliographystyle-link (limit)
"Find next bibliographystyle link up to LIMIT.
Add tooltip to the link."
(when (and (re-search-forward "bibliographystyle:\\([[:alnum:]]\\)\\{2,\\}" limit t)
(not (org-in-src-block-p))
(not (org-at-comment-p)))
(forward-char -2)
(let* ((this-link (org-element-context))
(path (org-element-property :path this-link))
(msg (shell-command-to-string (format "kpsewhich %s.bst" path))))
(add-text-properties
(org-element-property :begin this-link)
(- (org-element-property :end this-link)
(org-element-property :post-blank this-link))
(list
'help-echo msg))
(set-match-data
(list (org-element-property :begin this-link)
(- (org-element-property :end this-link)
(org-element-property :post-blank this-link))))
(goto-char (org-element-property :end this-link)))))
(defun org-ref-make-org-link-cite-key-visible (&rest _)
"Make the org-ref cite link visible in descriptive links."
(when (string-match-p "\\.org$\\|\\.txt$" (buffer-name))
(save-match-data
(let ((s (match-string 1))
(s-begin (match-beginning 1))
(s-end (match-end 1))
(beg (match-beginning 0))
(end (match-end 0))
(cite-re (format "^\\(%s:\\)"
(regexp-opt (-sort
(lambda (a b)
(> (length a) (length b)))
org-ref-cite-types))))
cite-type)
(when (and s (string-match cite-re s))
(setq cite-type (match-string 1 s))
(remove-text-properties beg end
'(invisible))
(add-text-properties
beg end
`(face (:foreground ,org-ref-cite-color))))))))
(when org-ref-colorize-links
(add-hook
'org-mode-hook
(lambda ()
(advice-add 'org-activate-bracket-links :after #'org-ref-make-org-link-cite-key-visible)
(font-lock-add-keywords
nil
'((org-ref-match-next-cite-link (0 'org-ref-cite-face t))
(org-ref-match-next-label-link (0 'org-ref-label-face t))
(org-ref-match-next-ref-link (0 'org-ref-ref-face t))
(org-ref-match-next-bibliography-link (0 'org-link t))
(org-ref-match-next-bibliographystyle-link (0 'org-link t)))
t)))))
;;* Links
;;** bibliography and bibliographystyle
(defun org-ref-open-bibliography-no-org (link-string)
"Open a bibliography link when you are not in org-mode.
This means you cannot use the usual org-machinery to figure it
out. We don't try to be clever here. If there is only one file,
we open it, otherwise prompt for which one to open."
(let ((bibfiles (split-string link-string ",")))
(find-file (if (= 1 (length bibfiles))
(car bibfiles)
(completing-read
"Bib file: " bibfiles nil t)))))
(defun org-ref-bibinputs ()
"Feed BIBINPUTS environment variable to `parse-colon-path'."
(parse-colon-path (getenv "BIBINPUTS")))