(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
+ "dark magenta"
+ "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-get-bibtex-keys ()
- "return a list of unique keys in the buffer."
+ "Return a list of unique keys in the buffer."
(let ((keys '()))
(org-element-map (org-element-parse-buffer) 'link
(lambda (link)
(key
(org-ref-split-and-strip-string (plist-get plist ':path)))
(when (not (-contains? keys key))
- (setq keys (append keys (list key)))))))))
+ (setq keys (append keys (list key))))))))
+ ;; set with-affiliated to get keys in captions
+ nil nil nil t)
;; Sort keys alphabetically
(setq keys (cl-sort keys 'string-lessp :key 'downcase))
keys))
#+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
(org-element-map (org-element-parse-buffer) 'link
(lambda (link)
(let ((plist (nth 1 link)))
- (when (equal (plist-get plist ':type) "cite")
- (dolist (key (org-ref-split-and-strip-string (plist-get plist ':path)) )
+ (when (-contains? org-ref-cite-types (plist-get plist :type))
+ (dolist (key (org-ref-split-and-strip-string (plist-get plist :path)))
(when (not (index key bibtex-keys))
- (setq bad-citations (append bad-citations
- `(,(format "%s [[elisp:(progn (switch-to-buffer-other-frame \"%s\")(goto-char %s))][not found here]]\n"
- key (buffer-name)(plist-get plist ':begin)))))
- ))))))
+ (message-box "%s" link)
+ (setq
+ bad-citations
+ (append
+ bad-citations
+ `(,(format "%s [[elisp:(progn (switch-to-buffer-other-frame \"%s\")(goto-char %s))][not found here]]\n"
+ key
+ (buffer-name)
+ (plist-get plist :begin)))))
+ )))))
+ ;; set with-affilates to t to get citations in a caption
+ nil nil nil t)
(if bad-citations
(progn
(org-element-map (org-element-parse-buffer) 'link
(lambda (link)
(let ((plist (nth 1 link)))
- (when (-contains? org-ref-cite-types (plist-get plist ':type))
- (dolist (key (org-ref-split-and-strip-string (plist-get plist ':path)) )
+ (when (-contains? org-ref-cite-types (plist-get plist :type))
+ (dolist (key (org-ref-split-and-strip-string (plist-get plist :path)) )
(when (not (index key bibtex-keys))
- (goto-char (plist-get plist ':begin))
+ (goto-char (plist-get plist :begin))
(re-search-forward key)
(push (cons key (point-marker)) bad-citations)))
- ))))
+ )))
+ ;; add with-affiliates to get cites in caption
+ nil nil nil t)
(goto-char cp)
bad-citations))
-;; It seems I forgot I already defined this earlier!
-;; (defun org-ref-get-labels ()
-;; "Returns a list of known labels in the org document. These include label links, latex labels, label tags, and table names. The list contains all labels, not just unique ones.
-;; "
-;; (let ((cp (point))
-;; (labels '()))
-;; (goto-char (point-min))
-;; (while (re-search-forward "[^#+]label:\\(.*\\)\\s-" nil t)
-;; (push (match-string 1) labels))
-
-;; (goto-char (point-min))
-;; (while (re-search-forward "\\label{\\(.*\\)}\\s-?" nil t)
-;; (push (match-string 1) labels))
-
-;; (goto-char (point-min))
-;; (while (re-search-forward "^#\\+label:\\s-*\\(.*\\)" nil t)
-;; (push (match-string 1) labels))
-
-;; (goto-char (point-min))
-;; (while (re-search-forward "^#\\+tblname:\\s-*\\(.*\\)" nil t)
-;; (push (match-string 1) labels))
-;; ;; check for CUSTOM_ID
-;; (org-map-entries
-;; (lambda ()
-;; (when (org-entry-get (point) "CUSTOM_ID")
-;; (push (org-entry-get (point) "CUSTOM_ID") labels))))
-;; ;; return to original place
-;; (goto-char cp)
-;; labels))
-
(defun org-ref-bad-ref-candidates ()
"Returns a list of conses (ref . marker) where ref is a ref link that does not point to anything (i.e. a label)."
* Helm interface
[[https://github.com/tmalsburg/helm-bibtex][helm-bibtex]] is a very cool interface to bibtex files. Out of the box though, it is not super convenient for org-ref. Here, we modify it to make it fit our workflow and extend it where needed.
+Let us add keywords as a searchable field.
+#+BEGIN_SRC emacs-lisp
+(setq helm-bibtex-additional-search-fields '(keywords))
+#+END_SRC
+
+Next, we are going to add keywords to the helm interface. This modifies the helm-bibtex function to add our keywords.
+#+BEGIN_SRC emacs-lisp
+(defun helm-bibtex-candidates-formatter (candidates source)
+ "Formats BibTeX entries for display in results list."
+ (cl-loop
+ with width = (with-helm-window (window-width))
+ for entry in candidates
+ for entry = (cdr entry)
+ for entry-key = (helm-bibtex-get-value entry 'entry-key)
+ for fields = (--map (helm-bibtex-clean-string
+ (helm-bibtex-get-value entry it " "))
+ '(author title year has-pdf has-note entry-type))
+ for fields = (-update-at 0 'helm-bibtex-shorten-authors fields)
+ for fields = (append fields
+ (list (or (helm-bibtex-get-value entry 'keywords)
+ "" )))
+ collect
+ (cons (s-format "$0 $1 $2 $3 $4$5 $6" 'elt
+ (-zip-with (lambda (f w) (truncate-string-to-width f w 0 ?\s))
+ fields (list 36 (- width 85) 4 1 1 7 7)))
+ entry-key)))
+
+#+END_SRC
+
+Next, we add some functions to add keywords to a bibtex entry using a helm interface, and a new action to add keywords to entries from helm-bibtex.
+#+BEGIN_SRC emacs-lisp
+;; adapted from bibtex-utils.el
+;; these are candidates for selecting keywords/tags
+(defun org-ref-bibtex-keywords ()
+ "Get keywords defined in current bibtex file.
+These are in the keywords field, and are comma or semicolon separated."
+ (save-excursion
+ (goto-char (point-min))
+ (let (keywords kstring)
+ (while (re-search-forward "^\\s-*keywords.*{\\([^}]+\\)}" nil t)
+ ;; TWS - remove newlines/multiple spaces:
+ (setq kstring (replace-regexp-in-string "[ \t\n]+" " " (match-string 1)))
+ (mapc
+ (lambda (v)
+ (add-to-list 'keywords v t))
+ (split-string kstring "\\(,\\|;\\)[ \n]*\\|{\\|}" t)))
+ keywords)))
+
+
+(defun org-ref-set-bibtex-keywords (keywords &optional arg)
+ "Add KEYWORDS to a bibtex entry.
+If KEYWORDS is a list, it is converted to a comma-separated string. The KEYWORDS are added to the beginning of the field. Otherwise KEYWORDS should be a string of comma-separate keywords."
+ (interactive "sKeywords: \nP")
+ (bibtex-set-field
+ "keywords"
+ (if arg
+ ;; replace with arg
+ (if (listp keywords)
+ (mapconcat 'identity keywords ", ")
+ keywords)
+ ;; else concatentate
+ (concat
+ (if (listp keywords)
+ (mapconcat 'identity keywords ", ")
+ keywords)
+ (when (not (string= "" (bibtex-autokey-get-field "keywords")))
+ (concat ", " (bibtex-autokey-get-field "keywords"))))))
+ (save-buffer))
+
+
+(defun helm-tag-bibtex-entry ()
+ "Helm interface to add keywords to a bibtex entry.
+Run this with the point in a bibtex entry."
+ (interactive)
+ (let ((keyword-source `((name . "Existing keywords")
+ (candidates . ,(org-ref-bibtex-keywords))
+ (action . (lambda (candidate)
+ (org-ref-set-bibtex-keywords
+ (mapconcat
+ 'identity
+ (helm-marked-candidates)
+ ", "))))))
+ (fallback-source `((name . "Add new keywords")
+ (dummy)
+ (action . (lambda (candidate)
+ (org-ref-set-bibtex-keywords helm-pattern)
+ )))))
+ (helm :sources '(keyword-source fallback-source))))
+
+
+(defun org-ref-helm-tag-entries (candidates)
+ "Set tags on selected bibtex entries from helm-bibtex.
+User is prompted for tags. This function is called from `helm-bibtex'."
+ (let ((keywords (read-input "Keywords (comma separated): ")))
+ (loop for key in (helm-marked-candidates)
+ do
+ (save-window-excursion
+ (helm-bibtex-show-entry key)
+ (bibtex-set-field
+ "keywords"
+ (concat
+ keywords
+ ", " (bibtex-autokey-get-field "keywords")))
+ (save-buffer)))))
+#+END_SRC
+
+Next, adapt the helm-bibtex source with these features:
+
1. Make the default action to insert selected keys.
2. Make open entry second action
+3. Add some features for adding keywords to bibtex entries.
+
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(setq helm-source-bibtex
'((name . "BibTeX entries")
("Show entry" . helm-bibtex-show-entry)
("Open PDF file (if present)" . helm-bibtex-open-pdf)
("Open URL or DOI in browser" . helm-bibtex-open-url-or-doi)
- ("Insert reference" . helm-bibtex-insert-reference)
+ ("Insert formatted reference" . helm-bibtex-insert-reference)
("Insert BibTeX key" . helm-bibtex-insert-key)
("Insert BibTeX entry" . helm-bibtex-insert-bibtex)
("Attach PDF to email" . helm-bibtex-add-PDF-attachment)
("Edit notes" . helm-bibtex-edit-notes)
+ ("Add keywords to entries" . org-ref-helm-tag-entries)
))))
#+END_SRC
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