4. Exportable links to LaTeX
5. Utility functions for dealing with bibtex files and org-files
+Some additional features include
+1. Get minibuffer messages for the cite/ref/label link under point
+
+With helm integration (default) you can:
+
+1. C-c ] to insert a citation link
+ in helm-bibtex
+ - Enter to insert or append citation(s)
+ - C-u Enter to insert an alternative cite link
+ - C-u C-u Enter to replace the citation at point
+2. C-u C-c ] to insert a ref link with helm completion
+3. C-u C-u C-c ] to insert a label with completion
+4. M-x org-ref to get a helm completion buffer with link checks, utilities and export options
+
** Header
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
;;; org-ref.el --- setup bibliography, cite, ref and label org-mode links.
(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
+
* 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-count-labels (label)
"Counts number of matches for label in the document"
- (+ (count-matches (format "label:%s\\b[^-:]" label) (point-min) (point-max) t)
+ (+ (count-matches (format "label:%s\\b[^-:]" label) (point-min) (point-max))
;; for tblname, it is not enough to get word boundary
;; tab-little and tab-little-2 match then.
- (count-matches (format "^#\\+tblname:\\s-*%s\\b[^-:]" label) (point-min) (point-max) t)
- (count-matches (format "\\label{%s}\\b" label) (point-min) (point-max) t)
+ (count-matches (format "^#\\+tblname:\\s-*%s\\b[^-:]" label) (point-min) (point-max))
+ (count-matches (format "\\label{%s}" label) (point-min) (point-max))
;; this is the org-format #+label:
- (count-matches (format "^#\\+label:\\s-*%s\\b[^-:]" label) (point-min) (point-max) t)
+ (count-matches (format "^#\\+label:\\s-*%s\\b[^-:]" label) (point-min) (point-max))
(let ((custom-id-count 0))
(org-map-entries
(lambda ()
- (when (string= label (org-entry-get (point) "CUSTOM_ID"))
+ (when (string= label (org-entry-get (point) "CUSTOM_ID"))
(setq custom-id-count (+ 1 custom-id-count)))))
custom-id-count)))
"label"
(lambda (label)
"on clicking count the number of label tags used in the buffer. A number greater than one means multiple labels!"
- (message (format "%s occurences" (org-ref-count-labels label))))
+ (let ((count (org-ref-count-labels label)))
+ (message (format "%s occurence%s"
+ count
+ (if (or (= count 0)
+ (> count 1))
+ "s"
+ ""))
+ (org-ref-count-labels label))))
(lambda (keyword desc format)
(cond
((eq format 'html) (format "(<label>%s</label>)" path))
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-ref-get-org-labels ()
- "find #+LABEL: labels"
+ "Return a list of #+LABEL: labels."
(save-excursion
(goto-char (point-min))
(let ((matches '()))
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-ref-get-custom-ids ()
- "return a list of custom_id properties in the buffer"
+ "Return a list of custom_id properties in the buffer."
(let ((results '()) custom_id)
(org-map-entries
(lambda ()
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-ref-get-tblnames ()
+ "Return list of table names in the buffer."
(org-element-map (org-element-parse-buffer 'element) 'table
(lambda (table)
(org-element-property :name table))))
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-ref-get-labels ()
- "returns a list of labels in the buffer that you can make a ref link to. this is used to auto-complete ref links."
+ "Returns a list of labels in the buffer that you can make a ref link to.
+This is used to auto-complete ref links and in helm menus."
(save-excursion
(save-restriction
(widen)
(goto-char (point-min))
(let ((matches '()))
- (while (re-search-forward "label:\\([a-zA-z0-9:-]*\\)" (point-max) t)
+ ;; these are the label:stuff kinds
+ (while (re-search-forward "[^#+]label:\\([a-zA-z0-9:-]*\\)" (point-max) t)
(add-to-list 'matches (match-string-no-properties 1) t))
- (append matches (org-ref-get-org-labels) (org-ref-get-latex-labels) (org-ref-get-tblnames) (org-ref-get-custom-ids))))))
+ (append matches
+ (org-ref-get-org-labels)
+ (org-ref-get-latex-labels)
+ (org-ref-get-tblnames)
+ (org-ref-get-custom-ids))))))
#+END_SRC
-Let us make a helm function to insert a label link. This will help you enter unique labels.
+Let us make a helm function to insert a label link. This will help you enter unique labels by showing matching labels until they are all gone and you are left with a unique one. If you are on a link, it means you want to replace it.
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-ref-helm-insert-label-link ()
"Insert a label link. helm just shows you what labels already exist.
helm-pattern))))))))))))
#+END_SRC
-Now we create the completion function. This works from the org-machinery, e.g. if you type C-c C-l to insert a link, and use completion by pressing tab.
+Now we create a completion function. This works from the org-machinery, e.g. if you type C-c C-l to insert a link, and use completion by pressing tab.
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-ref-complete-link (&optional arg)
"Helm menu to insert ref links to labels in the document.
If you are on link, replace with newly selected label.
Use C-u to insert a different kind of ref link.
+Use C-u C-u to insert a [[#custom-id]] link
"
(interactive)
(let* ((labels (org-ref-get-labels))
- (contexts (mapcar 'org-ref-get-label-context labels))
+ (bs (buffer-string))
+ (contexts (with-temp-buffer
+ (insert bs)
+ (mapcar 'org-ref-get-label-context labels)))
(cb (current-buffer)))
(helm :input (thing-at-point 'word)
(candidates . ("ref" "eqref" "pageref" "nameref"))
(action . (lambda (x) x))))
":" label)))
- ))))))))
+ ;; two prefixes, insert section custom-id link
+ ((equal helm-current-prefix-arg '(16))
+ (insert
+ (format "[[#%s]]" label)))
+ ))
+ ))))))
#+END_SRC
#+RESULTS:
;; 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)."
(progn
(forward-line 4)
(point)))))
- (beep)
(throw 'result "!!! NO CONTEXT FOUND !!!"))))
;; message some context about the label we are referring to
((string= type "ref")
- (message (org-ref-get-label-context
- (org-element-property :path object))))
+ (message "%scount: %s"
+ (org-ref-get-label-context
+ (org-element-property :path object))
+ (org-ref-count-labels
+ (org-element-property :path object))))
((string= type "eqref")
- (message (org-ref-get-label-context
- (org-element-property :path object))))
+ (message "%scount: %s"
+ (org-ref-get-label-context
+ (org-element-property :path object))
+ (org-ref-count-labels
+ (org-element-property :path object))))
;; message the count
((string= type "label")
(let ((count (org-ref-count-labels
(org-element-property :path object))))
;; get plurality on occurrence correct
- (when (> count 1) (beep))
(message (concat
(number-to-string count)
" occurence"
(> count 1))
"s")))))
+ ((string= type "custom-id")
+ (save-excursion
+ (org-open-link-from-string
+ (format "[[#%s]]" (org-element-property :path object)))
+ (message "%s" (org-get-heading))))
+
;; check if the bibliography files exist.
((string= type "bibliography")
(let* ((bibfile)
(buffer-substring key-beginning key-end)))
(if (file-exists-p bibfile)
(message "%s exists." bibfile)
- (beep)
(message "!!! %s NOT FOUND !!!" bibfile))))
)))))
#+END_SRC
(replace-regexp-in-string
(car (org-ref-get-bibtex-key-and-file)) ; key
(mapconcat 'identity keys ",") ; new keys
- (org-element-property :raw-link object)
- )
+ (org-element-property :raw-link object))
;; replace space at end to avoid collapsing into next word.
- last-char)))
+ last-char))
+ ;; and we want to go to the end of the new link
+ (goto-char
+ (org-element-property :end (org-element-context))))
(t
(message "Not found"))))
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
(insert-file-contents bibfile)
(bibtex-search-entry key)
(org-ref-bib-citation)))
- (beep)
"!!! No entry found !!!" )))
(defun org-ref-cite-candidates ()
projects / org-ref.git / blobdiff