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.
(require 'reftex-cite)
(require 'dash)
(require 'helm)
+(require 'helm-config)
(require 'helm-bibtex)
#+END_SRC
;; I do not remember why I put this next line in. It doesn't
;; work for org-files. Nothing very bad happens, but it gives
;; an annoying error. Commenting it out for now.
- ;(reftex-parse-all)
+ ;(reftex-parse-all
)
(make-local-variable 'reftex-cite-format)
- (setq reftex-cite-format 'org)
- (define-key org-mode-map (kbd org-ref-insert-cite-key) org-ref-insert-cite-function))
+ (setq reftex-cite-format 'org))
+
+;; define key for inserting citations
+(define-key org-mode-map
+ (kbd org-ref-insert-cite-key)
+ org-ref-insert-cite-function)
(add-hook 'org-mode-hook 'org-mode-reftex-setup)
(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.")
+
+
+(when org-ref-colorize-links
+ (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))
+#+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))
(let* ((bibfile)
;; object is the link you clicked on
(object (org-element-context))
-
(link-string-beginning)
(link-string-end))
#+END_SRC
** label
-The label link provides a way to create labels in org-mode. We make it clickable because we want to make sure labels are unique. This code will tell you how many instances of a label are found. We search for label links, LaTeX labels, and the org-mode format for labels. We probably should search for tblnames too.
-*************** TODO search tblnames, custom_ids and check for case sensitivity
-*************** END
+The label link provides a way to create labels in org-mode. We make it clickable because we want to make sure labels are unique. This code will tell you how many instances of a label are found. We search for label links, LaTeX labels, and org-mode format for labels, tblnames too.
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-
(defun org-ref-count-labels (label)
- (+ (count-matches (format "label:%s\\b[^-:]" label) (point-min) (point-max) t)
+ "Counts number of matches for label in the document"
+ (+ (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"))
+ (setq custom-id-count (+ 1 custom-id-count)))))
+ custom-id-count)))
(org-add-link-type
"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
-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.
+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.
+If you are on a label link, replace it."
+ (interactive)
+ (let* ((labels (org-ref-get-labels))
+ (cb (current-buffer)))
+ (helm :sources `(((name . "Existing labels")
+ (candidates . ,labels)
+ ;; default action is to open to the label
+ (action . (lambda (label)
+ ;; unfortunately I do not have markers here
+ (org-open-link-from-string (format "ref:%s" label))))
+ ;; if you select a label, replace current one
+ (action . (lambda (label)
+ (switch-to-buffer ,cb)
+ (cond
+ ;; no prefix or on a link
+ ((equal helm-current-prefix-arg nil)
+ (let* ((object (org-element-context))
+ (last-char (save-excursion
+ (goto-char (org-element-property :end object))
+ (backward-char)
+ (if (looking-at " ")
+ " "
+ ""))))
+ (when (-contains? '("label")
+ (org-element-property :type object))
+ ;; we are on a link, so replace it.
+ (setf
+ (buffer-substring
+ (org-element-property :begin object)
+ (org-element-property :end object))
+ (concat
+ (replace-regexp-in-string
+ (org-element-property :path object)
+ label
+ (org-element-property :raw-link object))
+ last-char)))))
+ ;; no prefix options defined
+ ))))
+ ;; no matching selection creates a new label
+ ((name . "Create new label")
+ (dummy)
+ ;; default action creates a new label, or replaces old one
+ (action . (lambda (label)
+ (switch-to-buffer ,cb)
+ (let* ((object (org-element-context))
+ (last-char (save-excursion
+ (goto-char (org-element-property :end object))
+ (backward-char)
+ (if (looking-at " ")
+ " "
+ ""))))
+ (if (-contains? '("label")
+ (org-element-property :type object))
+ ;; we are on a link, so replace it.
+ (setf
+ (buffer-substring
+ (org-element-property :begin object)
+ (org-element-property :end object))
+ (concat
+ (replace-regexp-in-string
+ (org-element-property :path object)
+ helm-pattern
+ (org-element-property :raw-link object))
+ last-char))
+ ;; new link
+ (insert
+ (concat
+ "label:"
+ (or label
+ helm-pattern))))))))))))
+#+END_SRC
+
+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)
(insert (org-ref-complete-link)))
#+END_SRC
+Another alternative ref insertion is to use helm.
+
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(defun org-ref-helm-insert-ref-link ()
+ "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))
+ (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)
+ :sources `(((name . "Available labels to ref")
+ (candidates . ,(loop for label in labels
+ for context in contexts
+ ;; we do some kludgy adding spaces
+ ;; and bars to make it "easier" to
+ ;; see in helm.
+ collect (cons (concat
+ label "\n"
+ (mapconcat
+ (lambda (x)
+ (concat " |" x))
+ (split-string context "\n")
+ "\n"
+ ) "\n\n") label)))
+ ;; default action to replace or insert ref link.
+ (action . (lambda (label)
+ (switch-to-buffer ,cb)
+
+ (cond
+ ;; no prefix or on a link
+ ((equal helm-current-prefix-arg nil)
+ (let* ((object (org-element-context))
+ (last-char (save-excursion
+ (goto-char (org-element-property :end object))
+ (backward-char)
+ (if (looking-at " ")
+ " "
+ ""))))
+ (if (-contains? '("ref" "eqref" "pageref" "nameref")
+ (org-element-property :type object))
+ ;; we are on a link, so replace it.
+ (setf
+ (buffer-substring
+ (org-element-property :begin object)
+ (org-element-property :end object))
+ (concat
+ (replace-regexp-in-string
+ (org-element-property :path object)
+ label
+ (org-element-property :raw-link object))
+ last-char))
+ ;; insert a new link
+ (insert
+ (concat
+ "ref:" label))
+ )))
+ ;; one prefix, alternate ref link
+ ((equal helm-current-prefix-arg '(4))
+ (insert
+ (concat
+ (helm :sources '((name . "Ref link types")
+ (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:
+: org-ref-helm-insert-ref-link
+
** pageref
This refers to the page of a label in LaTeX.
;; 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
(format "\\Glspl{%s}" path)))))
#+END_SRC
-
-
* Utilities
** create simple text citation from bibtex entry
*************** 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
#+END_SRC
** Find bad cite links
+ :PROPERTIES:
+ :ID: 8515E800-EDA0-4B2A-85FD-55B6FF849203
+ :END:
Depending on how you enter citations, you may have citations with no corresponding bibtex entry. This function finds them and gives you a clickable table to navigate to them.
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(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
(message "No bad cite links found"))))
#+END_SRC
+** helm interface to org-ref
+In [[id:8515E800-EDA0-4B2A-85FD-55B6FF849203][Find bad cite links]] we wrote a function that finds bad links and creates a buffer of links to them.
+
+Here we develop a similar idea, but instead of an org-buffer with links, we create helm sources for bad cite links, bad ref links, and multiple labels.
+
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(defun org-ref-bad-cite-candidates ()
+ "Returns a list of conses (key . marker) where key does not exist in the known bibliography files, and marker points to the key."
+ (let* ((cp (point)) ; save to return to later
+ (bibtex-files (org-ref-find-bibliography))
+ (bibtex-file-path (mapconcat
+ (lambda (x)
+ (file-name-directory (file-truename x)))
+ bibtex-files ":"))
+ (bibtex-keys (mapcar (lambda (x) (car x))
+ (bibtex-global-key-alist)))
+ (bad-citations '()))
+
+ (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 (not (index key bibtex-keys))
+ (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))
+
+
+(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)."
+ ;; first get a list of legitimate labels
+ (let ((cp (point))
+ (labels (org-ref-get-labels))
+ (bad-refs '()))
+ ;; now loop over ref links
+ (goto-char (point-min))
+ (org-element-map (org-element-parse-buffer) 'link
+ (lambda (link)
+ (let ((plist (nth 1 link)))
+ (when (or (equal (plist-get plist ':type) "ref")
+ (equal (plist-get plist ':type) "eqref")
+ (equal (plist-get plist ':type) "pageref")
+ (equal (plist-get plist ':type) "nameref"))
+ (unless (-contains? labels (plist-get plist :path))
+ (goto-char (plist-get plist :begin))
+ (add-to-list
+ 'bad-refs
+ (cons (plist-get plist :path)
+ (point-marker))))))))
+ (goto-char cp)
+ bad-refs))
+
+
+(defun org-ref-bad-label-candidates ()
+ "Return a list of labels where label is multiply defined."
+ (let ((labels (org-ref-get-labels))
+ (multiple-labels '()))
+ (when (not (= (length labels)
+ (length (-uniq labels))))
+ (dolist (label labels)
+ (when (> (-count (lambda (a)
+ (equal a label))
+ labels) 1)
+ ;; this is a multiply defined label.
+ (let ((cp (point)))
+ (goto-char (point-min))
+ (while (re-search-forward
+ (format "[^#+]label:%s\\s-" label) nil t)
+ (push (cons label (point-marker)) multiple-labels))
+
+ (goto-char (point-min))
+ (while (re-search-forward
+ (format "\\label{%s}\\s-?" label) nil t)
+ (push (cons label (point-marker)) multiple-labels))
+
+ (goto-char (point-min))
+ (while (re-search-forward
+ (format "^#\\+label:\\s-*%s" label) nil t)
+ (push (cons label (point-marker)) multiple-labels))
+
+ (goto-char (point-min))
+ (while (re-search-forward
+ (format "^#\\+tblname:\\s-*%s" label) nil t)
+ (push (cons label (point-marker)) multiple-labels))
+ (goto-char cp)))))
+ multiple-labels))
+#+END_SRC
+
+#+RESULTS:
+: org-ref-bad-label-candidates
+
+Now, we have a functions for candidates, we can make helm sources for each one, and then run a helm command to view them.
+
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(defun org-ref ()
+ "Opens a helm interface to actions for org-ref.
+Shows bad citations, ref links and labels"
+ (interactive)
+ (let ((cb (current-buffer))
+ (bad-citations (org-ref-bad-cite-candidates))
+ (bad-refs (org-ref-bad-ref-candidates))
+ (bad-labels (org-ref-bad-label-candidates)))
+
+ (helm :sources `(((name . "Bad citations")
+ (candidates . ,bad-citations)
+ (action . (lambda (marker)
+ (switch-to-buffer (marker-buffer marker))
+ (goto-char marker))))
+ ;;
+ ((name . "Bad Labels")
+ (candidates . ,bad-labels)
+ (action . (lambda (marker)
+ (switch-to-buffer (marker-buffer marker))
+ (goto-char marker))))
+ ;;
+ ((name . "Bad ref links")
+ (candidates . ,bad-refs)
+ (action . (lambda (marker)
+ (switch-to-buffer (marker-buffer marker))
+ (goto-char marker))))
+ ;;
+ ((name . "Utilities")
+ (candidates . (("Check buffer again" . org-ref)
+ ("Insert citation" . helm-bibtex)
+ ("Insert label link" . org-ref-helm-insert-label-link)
+ ("Insert ref link" . org-ref-helm-insert-ref-link)
+ ("List of figures" . org-ref-list-of-figures)
+ ("List of tables" . org-ref-list-of-tables)
+ ("Table of contents" . nil)
+ ))
+ (action . (lambda (x)
+ (switch-to-buffer ,cb)
+ (funcall x))))
+ ;;
+ ((name . "Export functions")
+ (candidates . (("Extract cited entries" . org-ref-extract-bibtex-entries)
+ ("Export to html and open" . (lambda () (org-open-file (org-html-export-to-html))))
+ ("Export to pdf and open" . (lambda ()
+ (org-open-file (org-latex-export-to-pdf))))
+ ("Export to manuscript pdf and open" . ox-manuscript-export-and-build-and-open)
+ ("Export submission manuscript pdf and open" . ox-manuscript-build-submission-manuscript-and-open)
+
+ ))
+ (action . (lambda (x)
+ (switch-to-buffer ,cb)
+ (funcall x))))
+ ))))
+#+END_SRC
+
+
** Finding non-ascii characters
I like my bibtex files to be 100% ascii. This function finds the non-ascii characters so you can replace them.
#+END_SRC
** Lightweight messages about links
-To get a lighter weight message about the label, ref and cite links, we define a function that gives us the minibuffer message, without the menu. We add it to a hook that updates after every command, including cursor movements.
-
-ref:test citep:test label:rett
+To get a lighter weight message about the label, ref and cite links, we define a function that gives us the minibuffer message, without the menu. We run this in an idle timer.
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-ref-get-label-context (label)
(point))
(progn
(forward-line 4)
- (point))))))))
+ (point)))))
+ (throw 'result "!!! NO CONTEXT FOUND !!!"))))
(defun org-ref-link-message ()
"Print a minibuffer message about the link that point is on."
(interactive)
- (let* ((object (org-element-context))
- (type (org-element-property :type object)))
-
- (cond
- ;; cite links
- ((-contains? org-ref-cite-types type)
- (message (org-ref-get-citation-string-at-point)))
-
- ;; 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 the count
- ((string= type "label")
- (let ((count (org-ref-count-labels
- (org-element-property :path object))))
- ;; get plurality on occurrence correct
- (message (concat
- (number-to-string count)
- " occurence"
- (when (or (= count 0)
- (> count 1))
- "s"))))))))
-
-
-(when org-ref-show-citation-on-enter
- (add-hook 'post-command-hook 'org-ref-link-message))
+ (when (eq major-mode 'org-mode)
+ (let* ((object (org-element-context))
+ (type (org-element-property :type object)))
+ (save-excursion
+ (cond
+ ;; cite links
+ ((-contains? org-ref-cite-types type)
+ (message (org-ref-get-citation-string-at-point)))
+
+ ;; message some context about the label we are referring to
+ ((string= type "ref")
+ (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 "%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
+ (message (concat
+ (number-to-string count)
+ " occurence"
+ (when (or (= count 0)
+ (> 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)
+ ;; object is the link you clicked on
+ (object (org-element-context))
+ (link-string (org-element-property :path object))
+ (link-string-beginning)
+ (link-string-end))
+ (save-excursion
+ (goto-char (org-element-property :begin object))
+ (search-forward link-string nil nil 1)
+ (setq link-string-beginning (match-beginning 0))
+ (setq link-string-end (match-end 0)))
+
+ ;; make sure we are in link and not before the :
+ (when (> link-string-beginning (point))
+ (goto-char link-string-beginning))
+
+ ;; now if we have comma separated bibliographies
+ ;; we find the one clicked on. we want to
+ ;; search forward to next comma from point
+ (save-excursion
+ (if (search-forward "," link-string-end 1 1)
+ (setq key-end (- (match-end 0) 1)) ; we found a match
+ (setq key-end (point)))) ; no comma found so take the point
+
+ ;; and backward to previous comma from point
+ (save-excursion
+ (if (search-backward "," link-string-beginning 1 1)
+ (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
+ (setq key-beginning (point)))) ; no match found
+ ;; save the key we clicked on.
+ (setq bibfile
+ (org-ref-strip-string
+ (buffer-substring key-beginning key-end)))
+ (if (file-exists-p bibfile)
+ (message "%s exists." bibfile)
+ (message "!!! %s NOT FOUND !!!" bibfile))))
+ )))))
#+END_SRC
* Aliases
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun helm-bibtex-format-org-ref (keys)
"Insert selected KEYS as cite link. Append KEYS if you are on a link.
-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."
- (let* ((object (org-element-context)))
+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.
+
+In the helm-bibtex buffer, C-u will give you a helm menu to select a new link type for the selected entries.
+
+C-u C-u will change the key at point to the selected keys.
+"
+ (let* ((object (org-element-context))
+ (last-char (save-excursion
+ (goto-char (org-element-property :end object))
+ (backward-char)
+ (if (looking-at " ")
+ " "
+ ""))))
(cond
;; case where we are in a link
((and (equal (org-element-type object) 'link)
(-contains?
org-ref-cite-types
(org-element-property :type object)))
- (goto-char (org-element-property :end object))
- ;; sometimes there are spaces at the end of the link
- ;; this code moves point pack until no spaces are there
- (while (looking-back " ") (backward-char))
- (insert (concat "," (mapconcat 'identity keys ","))))
+ (cond
+ ;; no prefix. append keys
+ ((equal helm-current-prefix-arg nil)
+ (goto-char (org-element-property :end object))
+ (while (looking-back " ") (backward-char))
+ (insert (concat "," (mapconcat 'identity keys ","))))
+ ;; double prefix, replace key at point
+ ((equal helm-current-prefix-arg '(16))
+ (setf (buffer-substring
+ (org-element-property :begin object)
+ (org-element-property :end object))
+ (concat
+ (replace-regexp-in-string
+ (car (org-ref-get-bibtex-key-and-file)) ; key
+ (mapconcat 'identity keys ",") ; new keys
+ (org-element-property :raw-link object))
+ ;; replace space at end to avoid collapsing into next word.
+ 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"))))
;; We are next to a link, and we want to append
+ ;; next to a link means one character back is on a link.
((save-excursion
(backward-char)
(and (equal (org-element-type (org-element-context)) 'link)
(-contains?
org-ref-cite-types
(org-element-property :type (org-element-context)))))
- (goto-char (org-element-property :end object))
(while (looking-back " ") (backward-char))
(insert (concat "," (mapconcat 'identity keys ","))))
;; insert fresh link
(t
+ ;;(message-box "fresh link")
(insert
- (concat (if helm-current-prefix-arg
- (ido-completing-read "Type: " org-ref-cite-types)
+ (concat (if (equal helm-current-prefix-arg '(4))
+ (helm :sources `((name . "link types")
+ (candidates . ,org-ref-cite-types)
+ (action . (lambda (x) x))))
org-ref-default-citation-link)
":"
(s-join "," keys))))))
-;; return empty string for helm
-"")
+ ;; return empty string for helm
+ "")
(setq helm-bibtex-format-citation-functions
'((org-mode . helm-bibtex-format-org-ref)))
-(defun org-ref-helm-insert-cite-link ()
- "org-ref function to use helm on the bibliography defined in the org-file."
- (interactive)
- (let ((helm-bibtex-bibliography (org-ref-find-bibliography)))
- (helm-bibtex)))
+(defun org-ref-helm-insert-cite-link (arg)
+ "org-ref function to use helm-bibtex to insert a citation link.
+With one prefix arg, insert a ref link.
+With two prefix args, insert a label link."
+ (interactive "P")
+ (cond
+ ((equal arg nil)
+ (let ((helm-bibtex-bibliography (org-ref-find-bibliography)))
+ (helm-bibtex)))
+ ((equal arg '(4))
+ (org-ref-helm-insert-ref-link))
+ ((equal arg '(16))
+ (org-ref-helm-insert-label-link))))
(require 'helm-bibtex)
+
+;; add our own fallback entries where we want them. These appear in reverse order of adding in the menu
+(setq helm-bibtex-fallback-options
+ (-insert-at 1 '("Crossref" . "http://search.crossref.org/?q=%s") helm-bibtex-fallback-options))
+
+(setq helm-bibtex-fallback-options
+ (-insert-at
+ 1
+ '("Scopus" . "http://www.scopus.com/scopus/search/submit/xadvanced.url?searchfield=TITLE-ABS-KEY(%s)")
+ helm-bibtex-fallback-options))
+
+(setq 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
(let* ((results (org-ref-get-bibtex-key-and-file))
(key (car results))
(bibfile (cdr results)))
- (save-excursion
- (with-temp-buffer
- (insert-file-contents bibfile)
- (bibtex-search-entry key)
- (org-ref-bib-citation)))))
+ (if bibfile
+ (save-excursion
+ (with-temp-buffer
+ (insert-file-contents bibfile)
+ (bibtex-search-entry key)
+ (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.
(when (string= doi "") (setq doi nil))
(when (string= url "") (setq url nil))
+ ;; Conditional pdf functions
(if (file-exists-p pdf-file)
(add-to-list
'candidates
'("Open pdf" . org-ref-open-pdf-at-point)
- t
- )
+ t)
(add-to-list
'candidates
'("Try to get pdf" . (lambda ()
'("Open notes" . org-ref-open-notes-at-point)
t)
+ ;; conditional url and doi functions
(when (or url doi)
(add-to-list
'candidates
projects / org-ref.git / blobdiff