(require 'reftex-cite)
(require 'dash)
(require 'helm)
+(require 'helm-config)
(require 'helm-bibtex)
#+END_SRC
(defcustom org-ref-cite-onclick-function
'org-ref-cite-click-helm
- "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."
+ "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'."
:type 'function
:group 'org-ref)
+
(defcustom org-ref-show-citation-on-enter t
"If non-nil add a hook function to show the citation summary in
the minibuffer just by putting the cursor in a link"
(kbd org-ref-insert-cite-key)
org-ref-insert-cite-function)
-(when org-ref-show-citation-on-enter
- (setq org-ref-message-timer
- (run-with-idle-timer 0.5 t 'org-ref-link-message)))
-
-(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)
- (setq org-ref-message-timer
- (run-with-idle-timer 0.5 t 'org-ref-link-message))
- )
-(defun org-ref-cancel-link-messages ()
- "Stop showing messages in minibuffer when on a link."
- (interactive)
- (cancel-timer org-ref-message-timer))
-
-;; this approach caused the selected region to not be highlighted any more.
-; (add-hook 'post-command-hook 'org-ref-link-message))
-; (remove-hook 'post-command-hook 'org-ref-link-message))
-
(add-hook 'org-mode-hook 'org-mode-reftex-setup)
(eval-after-load 'reftex-vars
(org-ref-define-citation-link "citez" ?z)
#+END_SRC
+** Messages for link at cursor
+Here we setup code that shows you a context message for the element under the cursor when emacs is idle.
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(defvar org-ref-message-timer nil
+ "Variable to store the link message timer in.")
+
+
+(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))))
+
+
+(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))
+
+
+(when org-ref-show-citation-on-enter
+ (org-ref-show-link-messages))
+
+;; this approach caused the selected region to not be highlighted any more.
+; (add-hook 'post-command-hook 'org-ref-link-message))
+; (remove-hook 'post-command-hook 'org-ref-link-message))
+#+END_SRC
+
+** Messages for context under mouse pointer
+Sometimes, when reading a document, I actually use the mouse more than the cursor. This code enables the mouse cursor to trigger a message in the minibuffer about what is under the cursor. I run this on a timer.
+
+The basic idea here is to get the mouse position, and if we can determine there is a character that (point) can move to, we move (point) and run the org-ref-link-message function. Since this runs on a timer, we store the last mouse position, and only run the function when the mouse has moved to avoid getting messages every time the timer runs.
+
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(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))))
+
+
+(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")
+
+
+(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))))
+
+
+(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"))
+#+END_SRC
+
+#+RESULTS:
+: org-ref-mouse-messages-off
+
+** Color-coded links
+Here we make the org-ref links a different color.
+
+citations are green
+refs are blue
+labels are black
+
+mailto:john
+
+cite:sokalski-2012-optim-ta,zhang-2011-spatial-tio2,li-2012-heter-ceram,li-2013-photoc
+
+cite*:sokalski-2012-optim-ta,zhang-2011-spatial-tio2,li-2012-heter-ceram,li-2013-photoc
+
+citenum:sokalski-2012-optim-ta,zhang-2011-spatial-tio2,li-2012-heter-ceram,li-2013-photoc
+
+ref:test
+
+label:test
+
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(defcustom org-ref-colorize-links
+ t
+ "When non-nil, change colors of links"
+ :group 'org-ref)
+
+
+(defcustom org-ref-cite-color
+ "forest green"
+ "Color of cite like links"
+ :group 'org-ref)
+
+
+(defcustom org-ref-ref-color
+ "dark red"
+ "Color of ref like links"
+ :group 'org-ref)
+
+
+(defcustom org-ref-label-color
+ "black"
+ "Color of label links"
+ :group 'org-ref)
+
+
+(defvar org-ref-cite-re nil
+ "regexp for cite links")
+
+
+(setq org-ref-cite-re
+ (concat "\\(" (mapconcat
+ (lambda (x)
+ (replace-regexp-in-string "\*" "\\\\*" x)
+ )
+ org-ref-cite-types "\\|") "\\)"
+ ":\\([a-zA-Z0-9-_:]*,?\\)*"))
+
+
+(setq org-ref-label-re
+ "label:\\([a-zA-Z0-9-_:]*,?\\)*")
+
+
+(setq org-ref-ref-re
+ "ref:\\([a-zA-Z0-9-_:]*,?\\)*")
+
+
+(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.")
+
+(defun org-ref-colorize-links ()
+ "Colorize org-ref links."
+ (hi-lock-mode 1)
+ (highlight-regexp org-ref-cite-re 'org-ref-cite-face)
+ (highlight-regexp org-ref-label-re 'org-ref-label-face)
+ (highlight-regexp org-ref-ref-re 'org-ref-ref-face))
+
+(when org-ref-colorize-links
+ (add-hook 'org-mode-hook 'org-ref-colorize-links))
+#+END_SRC
+
+#+RESULTS:
+
+
* Links
Most of this library is the creation of functional links to help with references and citations.
** General utilities
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-ref-key-in-file-p (key filename)
"determine if the key is in the file"
- (interactive "skey: \nsFile: ")
(save-current-buffer
(let ((bibtex-files (list filename)))
+ ;; This is something I am trying because when the bibtex file is open, and
+ ;; you have added to it, the only way I find to get the update to update
+ ;; is to close it and reopen it. or to save it and revert it.
+ (when (get-file-buffer filename)
+ (set-buffer (get-file-buffer filename))
+ (save-buffer)
+ (revert-buffer t t))
(bibtex-search-entry key t))))
#+END_SRC
(catch 'done
(let ((url (bibtex-autokey-get-field "url")))
(when url
- (browse-url url)
+ (browse-url (s-trim url))
(throw 'done nil)))
(let ((doi (bibtex-autokey-get-field "doi")))
(when doi
(if (string-match "^http" doi)
(browse-url doi)
- (browse-url (format "http://dx.doi.org/%s" doi)))
+ (browse-url (format "http://dx.doi.org/%s" (s-trim doi))))
(throw 'done nil))))))))
;; bibtex format
(concat "\\" ,type (when desc (org-ref-format-citation-description desc)) "{"
(mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
- "}"))))))
+ "}")))
+ ;; for markdown we generate pandoc citations
+ ((eq format 'md)
+ (cond
+ (desc ;; pre and or post text
+ (let* ((text (split-string desc "::"))
+ (pre (car text))
+ (post (cadr text)))
+ (concat
+ (format "[@%s," keyword)
+ (when pre (format " %s" pre))
+ (when post (format ", %s" post))
+ "]")))
+ (t
+ (format "[%s]"
+ (mapconcat
+ (lambda (key) (concat "@" key))
+ (org-ref-split-and-strip-string keyword)
+ "; "))))))))
#+END_SRC
*************** TODO document how to get the cookies
*************** END
-
-#+BEGIN_SRC python :tangle upload_bibtex_citeulike.py
+# :tangle upload_bibtex_citeulike.py
+#+BEGIN_SRC python
#!python
import pickle, requests, sys
helm-bibtex-fallback-options))
(setq helm-bibtex-fallback-options
- (-insert-at 1 '("Open Web of Science" . (lambda () (browse-url "http://apps.webofknowledge.com")))
- helm-bibtex-fallback-options))
+ (-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))
#+END_SRC
** A helm click menu
(org-ref-bib-citation)))
"!!! No entry found !!!" )))
+
(defun org-ref-cite-candidates ()
"Generate the list of possible candidates for click actions on a cite link.
Checks for pdf and doi, and add appropriate functions."
#+RESULTS:
: org-ref-cite-click-helm
+** A hydra click interface
+I like hydra a lot. Here we define a hydra menu you might like for the link click action.
+
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(when (featurep 'hydra)
+ (require 'hydra)
+ (setq hydra-is-helpful t)
+
+ (defhydra org-ref-cite-hydra (:color blue)
+ "
+_p_: Open pdf _w_: WOS _g_: Google Scholar _K_: Copy citation to clipboard
+_u_: Open url _r_: WOS related _P_: Pubmed _k_: Copy key to clipboard
+_n_: Open notes _c_: WOS citing _C_: Crossref _f_: Copy bibtex entry to file
+_o_: Open entry _e_: Email entry and pdf
+"
+ ("o" org-ref-open-citation-at-point nil)
+ ("p" org-ref-open-pdf-at-point nil)
+ ("n" org-ref-open-notes-at-point nil)
+ ("u" org-ref-open-url-at-point nil)
+ ("w" org-ref-wos-at-point nil)
+ ("r" org-ref-wos-related-at-point nil)
+ ("c" org-ref-wos-citing-at-point nil)
+ ("g" org-ref-google-scholar-at-point nil)
+ ("P" org-ref-pubmed-at-point nil)
+ ("C" org-ref-crossref-at-point nil)
+ ("K" org-ref-copy-entry-as-summary nil)
+ ("k" (progn
+ (kill-new
+ (car (org-ref-get-bibtex-key-and-file)))) nil)
+ ("f" org-ref-copy-entry-at-point-to-file nil)
+
+ ("e" (save-excursion
+ (org-ref-open-citation-at-point)
+ (email-bibtex-entry)) nil)))
+#+END_SRC
+
* End of code
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(provide 'org-ref)
projects / org-ref.git / blobdiff