rm interactive on org-ref-key-in-file
[org-ref.git] / org-ref.org
index 28ea7d8..8852a84 100644 (file)
@@ -7,11 +7,25 @@
 This document is an experiment at creating a literate program to provide similar features as reftex for org-mode referencing. These features include:
 
 1. using completion to create links
-2. storing links to places, 
+2. storing links to places,
 3. Clickable links that do useful things
 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.
@@ -38,11 +52,11 @@ This document is an experiment at creating a literate program to provide similar
 
 ;;; Commentary:
 ;;
-;; Lisp code to setup bibliography cite, ref and label org-mode links.
-;; also sets up reftex for org-mode. The links are clickable and do
-;; things that are useful. You should really read org-ref.org for details.
+;; 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 for details.
 ;;
-;; Package-Requires: ((dash))
+;; Package-Requires: ((dash) (helm) (helm-bibtex))
 #+END_SRC
 
 ** requires
@@ -51,6 +65,9 @@ The only external require is reftex-cite
 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
 (require 'reftex-cite)
 (require 'dash)
+(require 'helm)
+(require 'helm-config)
+(require 'helm-bibtex)
 #+END_SRC
 
 ** Custom variables
@@ -113,7 +130,36 @@ There are some variables needed later to tell this library where you store your
     ;;(org-tree-to-indirect-buffer)
     (outline-previous-visible-heading 1)
     (recenter-top-bottom 0))
-  "User-defined way to open a notes entry. This is excecuted after the entry is found, 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") 
+  "User-defined way to open a notes entry. This is excecuted after the entry is found, 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-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-insert-cite-function
+  'org-ref-helm-insert-cite-link
+  "Function to call to insert citation links. The default is `org-ref-helm-insert-cite-link' which uses `helm-bibtex'. org-ref modifies helm-bibtex a little bit to give org-mode citations, and to reorder default actions. You may use `org-ref-insert-cite-link' if you like the reftex interface."
+ :type 'function
+ :group 'org-ref)
+
+
+(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."
+ :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"
+ :group 'org-ref)
+
 #+END_SRC
 
 This next variable determines the citation types that are available in org-ref. Links for each one are automatically generated, and completion functions are automatically generated. Users may add to this list in their own init files.
@@ -187,11 +233,15 @@ We setup reftex here. We use a custom insert cite link function defined here: [[
         ;; 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-link))
+    (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)
 
@@ -214,7 +264,7 @@ We setup reftex here. We use a custom insert cite link function defined here: [[
                          )))))
 #+END_SRC
 
-You may want to add new formats to the reftex-cite-format-builtin variable. Here is an example of adding two new formats. Note that this does not create the links. 
+You may want to add new formats to the reftex-cite-format-builtin variable. Here is an example of adding two new formats. Note that this does not create the links.
 
 #+BEGIN_SRC emacs-lisp :tangle no
 ;; add new format
@@ -228,6 +278,189 @@ You can define a new citation link like this:
 (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
@@ -263,7 +496,7 @@ Reftex is no longer being developed. I want a url and doi option for formatting,
     (when (and (not (string= result "")) (string= "{" (substring result 0 1)))
       (setq result (substring result 1 -1)))
     (when (and (not (string= result "")) (string= "\"" (substring result 0 1)))
-      (setq result (substring result 1 -1)))    
+      (setq result (substring result 1 -1)))
       result))
 
 (defun org-ref-reftex-format-citation (entry format)
@@ -380,7 +613,7 @@ environment, only %l is available."
 
     (setq file (catch 'result
                 (loop for file in org-ref-bibliography-files do
-                      (if (org-ref-key-in-file-p key (file-truename file)) 
+                      (if (org-ref-key-in-file-p key (file-truename file))
                           (throw 'result file)
                         (message "%s not found in %s" key (file-truename file))))))
 
@@ -394,7 +627,7 @@ environment, only %l is available."
          (setq entry  (org-ref-reftex-format-citation bibtex-entry format))
        (save-restriction
          (bibtex-narrow-to-entry)
-         (setq entry (buffer-string)))))      
+         (setq entry (buffer-string)))))
     entry))
 #+END_SRC
 
@@ -416,17 +649,19 @@ This code provides some functions to generate a simple sorted bibliography in ht
 
 #+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)       
-       (let ((plist (nth 1 link)))                          
+      (lambda (link)
+       (let ((plist (nth 1 link)))
          (when (-contains? org-ref-cite-types (plist-get plist ':type))
-           (dolist 
-               (key 
+           (dolist
+               (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))
@@ -443,7 +678,7 @@ This function gets the html for one entry.
 
 Now, we map over the whole list of keys, and the whole bibliography, formatted as an unordered list.
 
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el 
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
 (defun org-ref-get-html-bibliography ()
   "Create an html bibliography when there are keys"
   (let ((keys (org-ref-get-bibtex-keys)))
@@ -468,7 +703,7 @@ First, we get the string for a single entry.
 
     (setq file (catch 'result
                 (loop for file in org-ref-bibliography-files do
-                      (if (org-ref-key-in-file-p key (file-truename file)) 
+                      (if (org-ref-key-in-file-p key (file-truename file))
                           (throw 'result file)
                         (message "%s not found in %s" key (file-truename file))))))
 
@@ -491,7 +726,7 @@ First, we get the string for a single entry.
 #+END_SRC
 
 Now, we loop over the keys, and combine all the entries into a bibliography.
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el 
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
 (defun org-ref-get-org-bibliography ()
   "Create an org bibliography when there are keys"
   (let ((keys (org-ref-get-bibtex-keys)))
@@ -515,12 +750,12 @@ This function gets the html for one entry.
 
 Now, we map over the whole list of keys, and the whole bibliography, formatted as an unordered list.
 
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el 
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
 (defun org-ref-get-ascii-bibliography ()
   "Create an html bibliography when there are keys"
   (let ((keys (org-ref-get-bibtex-keys)))
     (when keys
-      (concat 
+      (concat
 "Bibliography
 =============
 "
@@ -537,15 +772,14 @@ We use a link for the bibliography so that we can click on it to open the biblio
                   ;; this code is run on clicking. The bibliography
                   ;; may contain multiple files. this code finds the
                   ;; one you clicked on and opens it.
-                  (lambda (link-string)        
+                  (lambda (link-string)
                       ;; get link-string boundaries
                       ;; we have to go to the beginning of the line, and then search forward
-                      
+
                     (let* ((bibfile)
                            ;; object is the link you clicked on
                            (object (org-element-context))
-                           (link-string-beginning) 
+                           (link-string-beginning)
                            (link-string-end))
 
                     (save-excursion
@@ -558,7 +792,7 @@ We use a link for the bibliography so that we can click on it to open the biblio
                       ;; here. it should be a local variable only in
                       ;; the current buffer. We need this for using
                       ;; reftex to do citations.
-                      (set (make-local-variable 'reftex-default-bibliography) 
+                      (set (make-local-variable 'reftex-default-bibliography)
                            (split-string (org-element-property :path object) ","))
 
                       ;; now if we have comma separated bibliographies
@@ -584,12 +818,12 @@ We use a link for the bibliography so that we can click on it to open the biblio
                       ((eq format 'ascii) (org-ref-get-ascii-bibliography))
                      ((eq format 'html) (org-ref-get-html-bibliography))
                      ((eq format 'latex)
-                      ;; write out the latex bibliography command                     
+                      ;; write out the latex bibliography command
                       (format "\\bibliography{%s}" (replace-regexp-in-string  "\\.bib" "" (mapconcat 'identity
                                                                                                      (mapcar 'expand-file-name
                                                                                                              (split-string keyword ","))
                                                                                                      ",")))))))
-                                                                              
+
 #+END_SRC
 
 Believe it or not, sometimes it makes sense /not/ to include the bibliography in a document (e.g. when you are required to submit references as a separate file). To generate the references,  in another file, you must make a little tex file with these contents, and then compile it.
@@ -605,15 +839,15 @@ Here, we make a =nobibliography= link that acts like the bibliography, enables c
                   ;; this code is run on clicking. The bibliography
                   ;; may contain multiple files. this code finds the
                   ;; one you clicked on and opens it.
-                  (lambda (link-string)        
+                  (lambda (link-string)
                       ;; get link-string boundaries
                       ;; we have to go to the beginning of the line, and then search forward
-                      
+
                     (let* ((bibfile)
                            ;; object is the link you clicked on
                            (object (org-element-context))
-                           (link-string-beginning) 
+
+                           (link-string-beginning)
                            (link-string-end))
 
                     (save-excursion
@@ -626,7 +860,7 @@ Here, we make a =nobibliography= link that acts like the bibliography, enables c
                       ;; here. it should be a local variable only in
                       ;; the current buffer. We need this for using
                       ;; reftex to do citations.
-                      (set (make-local-variable 'reftex-default-bibliography) 
+                      (set (make-local-variable 'reftex-default-bibliography)
                            (split-string (org-element-property :path object) ","))
 
                       ;; now if we have comma separated bibliographies
@@ -652,7 +886,7 @@ Here, we make a =nobibliography= link that acts like the bibliography, enables c
                       ((eq format 'ascii) (org-ref-get-ascii-bibliography))
                      ((eq format 'html) (org-ref-get-html-bibliography))
                      ((eq format 'latex)
-                      ;; write out the latex bibliography command                     
+                      ;; write out the latex bibliography command
 
 ;                     (format "{\\setbox0\\vbox{\\bibliography{%s}}}"
 ;                             (replace-regexp-in-string  "\\.bib" "" (mapconcat 'identity
@@ -666,7 +900,7 @@ Here, we make a =nobibliography= link that acts like the bibliography, enables c
                                                                                         (split-string keyword ","))
                                                                                 ",")))
 
-                      ))))                                                                            
+                      ))))
 #+END_SRC
 
 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
@@ -695,7 +929,7 @@ We also create a bibliographystyle link. There is nothing to do on clicking here
 #+END_SRC
 
 *** Completion for bibliography link
-It would be nice 
+It would be nice
 
 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
 (defun org-bibliography-complete-link (&optional arg)
@@ -714,15 +948,15 @@ This is apparently used for biblatex.
                   ;; this code is run on clicking. The addbibresource
                   ;; may contain multiple files. this code finds the
                   ;; one you clicked on and opens it.
-                  (lambda (link-string)        
+                  (lambda (link-string)
                       ;; get link-string boundaries
                       ;; we have to go to the beginning of the line, and then search forward
-                      
+
                     (let* ((bibfile)
                            ;; object is the link you clicked on
                            (object (org-element-context))
-                           (link-string-beginning) 
+
+                           (link-string-beginning)
                            (link-string-end))
 
                     (save-excursion
@@ -735,7 +969,7 @@ This is apparently used for biblatex.
                       ;; here. it should be a local variable only in
                       ;; the current buffer. We need this for using
                       ;; reftex to do citations.
-                      (set (make-local-variable 'reftex-default-addbibresource) 
+                      (set (make-local-variable 'reftex-default-addbibresource)
                            (split-string (org-element-property :path object) ","))
 
                       ;; now if we have comma separated bibliographies
@@ -774,27 +1008,27 @@ In long documents, a list of figures is not uncommon. Here we create a clickable
   (save-excursion (widen)
   (let* ((c-b (buffer-name))
         (counter 0)
-        (list-of-figures 
+        (list-of-figures
          (org-element-map (org-element-parse-buffer) 'link
-           (lambda (link) 
+           (lambda (link)
              "create a link for to the figure"
-             (when 
+             (when
                  (and (string= (org-element-property :type link) "file")
-                      (string-match-p  
+                      (string-match-p
                        "[^.]*\\.\\(png\\|jpg\\|eps\\|pdf\\)$"
-                       (org-element-property :path link)))                   
+                       (org-element-property :path link)))
                (incf counter)
-               
+
                (let* ((start (org-element-property :begin link))
                       (parent (car (cdr (org-element-property :parent link))))
                       (caption (caaar (plist-get parent :caption)))
                       (name (plist-get parent :name)))
-                 (if caption 
-                     (format 
-                      "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]] %s\n" 
+                 (if caption
+                     (format
+                      "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]] %s\n"
                       c-b start counter (or name "") caption)
-                   (format 
-                    "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]]\n" 
+                   (format
+                    "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]]\n"
                     c-b start counter (or name "")))))))))
     (switch-to-buffer "*List of Figures*")
     (setq buffer-read-only nil)
@@ -805,7 +1039,7 @@ In long documents, a list of figures is not uncommon. Here we create a clickable
     (use-local-map (copy-keymap org-mode-map))
     (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
 
-(org-add-link-type 
+(org-add-link-type
  "list-of-figures"
  'org-ref-list-of-figures ; on click
  (lambda (keyword desc format)
@@ -824,20 +1058,20 @@ In long documents, a list of figures is not uncommon. Here we create a clickable
   (widen)
   (let* ((c-b (buffer-name))
         (counter 0)
-        (list-of-tables 
+        (list-of-tables
          (org-element-map (org-element-parse-buffer 'element) 'table
-           (lambda (table) 
+           (lambda (table)
              "create a link for to the table"
              (incf counter)
              (let ((start (org-element-property :begin table))
                    (name  (org-element-property :name table))
                    (caption (caaar (org-element-property :caption table))))
-               (if caption 
-                   (format 
-                    "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]] %s\n" 
+               (if caption
+                   (format
+                    "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]] %s\n"
                     c-b start counter (or name "") caption)
-                 (format 
-                  "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]]\n" 
+                 (format
+                  "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]]\n"
                   c-b start counter (or name ""))))))))
     (switch-to-buffer "*List of Tables*")
     (setq buffer-read-only nil)
@@ -848,7 +1082,7 @@ In long documents, a list of figures is not uncommon. Here we create a clickable
     (use-local-map (copy-keymap org-mode-map))
     (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
 
-(org-add-link-type 
+(org-add-link-type
  "list-of-tables"
  'org-ref-list-of-tables
  (lambda (keyword desc format)
@@ -858,23 +1092,37 @@ In long documents, a list of figures is not uncommon. Here we create a clickable
 #+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)
+  "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))
+     (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))
+     (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"
-                   (+ (count-matches (format "label:%s\\b[^-:]" label) (point-min) (point-max) t)
-                       ;; 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)
-                       ;; this is the org-format #+label:
-                      (count-matches (format "^#\\+label:\\s-*%s\\b[^-:]" label) (point-min) (point-max) t)))))
+   (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))
@@ -887,9 +1135,9 @@ We want to store links on labels, so you can put the cursor on the label, press
 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
 (defun org-label-store-link ()
   "store a link to a label. The output will be a ref to that label"
-  ;; First we have to make sure we are on a label link. 
+  ;; First we have to make sure we are on a label link.
   (let* ((object (org-element-context)))
-    (when (and (equal (org-element-type object) 'link) 
+    (when (and (equal (org-element-type object) 'link)
                (equal (org-element-property :type object) "label"))
       (org-store-link-props
        :type "ref"
@@ -921,7 +1169,7 @@ We want to store links on labels, so you can put the cursor on the label, press
 #+END_SRC
 ** ref
 
-The ref link allows you make links to labels. Clicking on the link takes you to the label, and provides a mark to go back to. 
+The ref link allows you make links to labels. Clicking on the link takes you to the label, and provides a mark to go back to.
 
 At the moment, ref links are not usable for section links. You need [[#CUSTOM_ID]] type links.
 
@@ -939,7 +1187,7 @@ At the moment, ref links are not usable for section links. You need [[#CUSTOM_ID
    (unless
        (or
        ;; our label links
-       (progn 
+       (progn
          (goto-char (point-min))
          (re-search-forward (format "label:%s\\b" label) nil t))
 
@@ -952,7 +1200,7 @@ At the moment, ref links are not usable for section links. You need [[#CUSTOM_ID
        (progn
          (goto-char (point-min))
          (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
-       
+
        ;; org tblname
        (progn
          (goto-char (point-min))
@@ -982,7 +1230,7 @@ It would be nice to use completion to enter a ref link, where a list of labels i
 
 #+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 '()))
@@ -993,10 +1241,10 @@ 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 () 
+   (org-map-entries
+    (lambda ()
       (let ((custom_id (org-entry-get (point) "CUSTOM_ID")))
        (when (not (null custom_id))
          (setq results (append results (list custom_id)))))))
@@ -1018,8 +1266,9 @@ Finally, we get the table names.
 
 #+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) 
+    (lambda (table)
       (org-element-property :name table))))
 #+END_SRC
 
@@ -1027,18 +1276,100 @@ Now, we can put all the labels together which will give us a list of candidates.
 
 #+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)
@@ -1056,6 +1387,89 @@ Alternatively, you may want to just call a function that inserts a link with com
  (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.
@@ -1071,7 +1485,7 @@ This refers to the page of a label in LaTeX.
    (unless
        (or
        ;; our label links
-       (progn 
+       (progn
          (goto-char (point-min))
          (re-search-forward (format "label:%s\\b" label) nil t))
 
@@ -1084,7 +1498,7 @@ This refers to the page of a label in LaTeX.
        (progn
          (goto-char (point-min))
          (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
-       
+
        ;; org tblname
        (progn
          (goto-char (point-min))
@@ -1158,7 +1572,7 @@ The nameref link allows you make links to the text of a section with a label. Cl
 
 ** eqref
 This is just the LaTeX ref for equations. On export, the reference is enclosed in parentheses.
+
 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
 (org-add-link-type
  "eqref"
@@ -1203,7 +1617,7 @@ point to get a comma, or the end of the link, and then backwards
 to get a comma, or the beginning of the link. that delimits the
 keyword we clicked on. We also strip the text properties."
   (interactive)
-  (let* ((object (org-element-context))         
+  (let* ((object (org-element-context))
         (link-string (org-element-property :path object)))
     ;; you may click on the part before the citations. here we make
     ;; sure to move to the beginning so you get the first citation.
@@ -1214,10 +1628,10 @@ keyword we clicked on. We also strip the text properties."
       ;; check if we clicked before the path and move as needed.
       (unless (< cp (point))
        (goto-char cp)))
-       
+
     (if (not (org-element-property :contents-begin object))
        ;; this means no description in the link
-       (progn    
+       (progn
          ;; we need the link path start and end
          (save-excursion
            (goto-char (org-element-property :begin object))
@@ -1266,14 +1680,14 @@ falling back to what the user has set in org-ref-default-bibliography
              (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
        (throw 'result org-ref-bibliography-files))
 
-      
+
       ;; we did not find a bibliography link. now look for \bibliography
       (goto-char (point-min))
       (when (re-search-forward "\\\\bibliography{\\([^}]+\\)}" nil t)
        ;; split, and add .bib to each file
        (setq org-ref-bibliography-files
              (mapcar (lambda (x) (concat x ".bib"))
-                     (mapcar 'org-ref-strip-string 
+                     (mapcar 'org-ref-strip-string
                              (split-string (match-string 1) ","))))
        (throw 'result org-ref-bibliography-files))
 
@@ -1284,7 +1698,7 @@ falling back to what the user has set in org-ref-default-bibliography
        (setq org-ref-bibliography-files
              (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
        (throw 'result org-ref-bibliography-files))
-         
+
       ;; we did not find anything. use defaults
       (setq org-ref-bibliography-files org-ref-default-bibliography)))
 
@@ -1294,14 +1708,20 @@ falling back to what the user has set in org-ref-default-bibliography
 #+END_SRC
 
 **** Finding the bibliography file a key is in
-Now, we can see if an entry is in a file. 
+Now, we can see if an entry is in a file.
 
 #+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
 
@@ -1317,7 +1737,7 @@ Finally, we want to know which file the key is in.
      (setq key (org-ref-get-bibtex-key-under-cursor)))
    (setq file     (catch 'result
                    (loop for file in org-ref-bibliography-files do
-                         (if (org-ref-key-in-file-p key (file-truename file)) 
+                         (if (org-ref-key-in-file-p key (file-truename file))
                              (throw 'result file)))))
    (cons key file)))
 #+END_SRC
@@ -1385,7 +1805,7 @@ We need some convenience functions to open act on the citation at point. These w
   (let* ((cb (current-buffer))
        (results (org-ref-get-bibtex-key-and-file))
        (key (car results))
-       (bibfile (cdr results)))        
+       (bibfile (cdr results)))
     (message "%s" (progn
                    (with-temp-buffer
                       (insert-file-contents bibfile)
@@ -1406,30 +1826,69 @@ We need some convenience functions to open act on the citation at point. These w
 
 **** the actual minibuffer menu
 Now, we create the menu. This is a rewrite of the cite action. This makes the function extendable by users.
+
 #+BEGIN_SRC emacs-lisp  :tangle org-ref.el
 (defvar org-ref-cite-menu-funcs '()
- "Functions to run on cite click menu. Each entry is a list of (key menu-name function). 
+ "Functions to run on cite click menu. Each entry is a list of (key menu-name function).
 The function must take no arguments and work on the key at point. Do not modify this variable, it is set to empty in the menu click function, and functions are conditionally added to it.")
 
 
 (defvar org-ref-user-cite-menu-funcs
-  '(("C" "rossref" org-ref-crossref-at-point))
+  '(("C" "rossref" org-ref-crossref-at-point)
+    ("y" "Copy entry to file" org-ref-copy-entry-at-point-to-file)
+    ("s" "Copy summary" org-ref-copy-entry-as-summary))
   "user-defined functions to run on bibtex key at point.")
 
 
+(defun org-ref-copy-entry-as-summary ()
+  "Copy the bibtex entry for the citation at point as a summary."
+  (interactive)
+    (save-window-excursion
+      (org-ref-open-citation-at-point)
+      (kill-new (org-ref-bib-citation))))
+
+
+(defun org-ref-copy-entry-at-point-to-file ()
+  "Copy the bibtex entry for the citation at point to NEW-FILE.
+Prompt for NEW-FILE includes bib files in org-ref-default-bibliography, and bib files in current working directory. You can also specify a new file."
+  (interactive)
+  (let ((new-file (ido-completing-read
+                  "Copy to bibfile: "
+                  (append org-ref-default-bibliography
+                          (f-entries "." (lambda (f) (f-ext? f "bib"))))))
+       (key (org-ref-get-bibtex-key-under-cursor)))
+    (save-window-excursion
+      (org-ref-open-citation-at-point)
+      (bibtex-copy-entry-as-kill))
+
+    (let ((bibtex-files (list (file-truename new-file))))
+      (if (assoc key (bibtex-global-key-alist))
+         (message "That key already exists in %s" new-file)
+       ;; add to file
+       (save-window-excursion
+         (find-file new-file)
+         (goto-char (point-max))
+          ;; make sure we are at the beginning of a line.
+         (unless (looking-at "^") (insert "\n\n"))
+         (bibtex-yank)
+         (save-buffer))))))
+
+
 (defun org-ref-get-doi-at-point ()
   "Get doi for key at point."
   (interactive)
   (let* ((results (org-ref-get-bibtex-key-and-file))
         (key (car results))
-        (bibfile (cdr results)))
+        (bibfile (cdr results))
+         doi)
     (save-excursion
       (with-temp-buffer
         (insert-file-contents bibfile)
         (bibtex-search-entry key)
-          (bibtex-autokey-get-field "doi")))))
-  
+       (setq doi (bibtex-autokey-get-field "doi"))
+       ;; in case doi is a url, remove the url part.
+       (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))))
+
 
 ;; functions that operate on key at point for click menu
 (defun org-ref-wos-at-point ()
@@ -1479,24 +1938,24 @@ Provides a menu of context sensitive actions. If the bibtex entry has a pdf, you
         (url (save-excursion
                (with-temp-buffer
                  (insert-file-contents bibfile)
-                 (bibtex-search-entry key)             
+                 (bibtex-search-entry key)
                  (bibtex-autokey-get-field "url"))))
         (doi (save-excursion
                (with-temp-buffer
                  (insert-file-contents bibfile)
                  (bibtex-search-entry key)
                  ;; I like this better than bibtex-url which does not always find
-                 ;; the urls             
+                 ;; the urls
                  (bibtex-autokey-get-field "doi")))))
 
     (when (string= "" doi) (setq doi nil))
     (when (string= "" url) (setq url nil))
     (setq org-ref-cite-menu-funcs '())
-        
+
     ;; open action
     (when
        bibfile
-      (add-to-list 
+      (add-to-list
        'org-ref-cite-menu-funcs
        '("o" "pen" org-ref-open-citation-at-point)))
 
@@ -1504,7 +1963,7 @@ Provides a menu of context sensitive actions. If the bibtex entry has a pdf, you
     (when (file-exists-p pdf-file)
       (add-to-list
        'org-ref-cite-menu-funcs
-       '("p" "df" org-ref-open-pdf-at-point) t))
+       `("p" "df" ,org-ref-open-pdf-function) t))
 
     ;; notes
     (add-to-list
@@ -1530,7 +1989,7 @@ Provides a menu of context sensitive actions. If the bibtex entry has a pdf, you
       (add-to-list
        'org-ref-cite-menu-funcs
        '("r" "elated" org-ref-wos-related-at-point) t)
-      
+
       (add-to-list
        'org-ref-cite-menu-funcs
        '("g" "oogle scholar" org-ref-google-scholar-at-point) t)
@@ -1549,16 +2008,25 @@ Provides a menu of context sensitive actions. If the bibtex entry has a pdf, you
     (add-to-list
      'org-ref-cite-menu-funcs
      '("q" "uit" (lambda ())) t)
-      
+
     ;; now we make a menu
     ;; construct menu string as a message
     (message
      (concat
+      (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))))
+      "\n"
       (mapconcat
        (lambda (tup)
         (concat "[" (elt tup 0) "]"
                 (elt tup 1) " "))
-       org-ref-cite-menu-funcs "") ": "))
+       org-ref-cite-menu-funcs "")))
     ;; get the input
     (let* ((input (read-char-exclusive))
           (choice (assoc
@@ -1566,11 +2034,14 @@ Provides a menu of context sensitive actions. If the bibtex entry has a pdf, you
       ;; now run the function (2nd element in choice)
       (when choice
        (funcall
-        (elt 
+        (elt
          choice
          2))))))
 #+END_SRC
 
+#+RESULTS:
+: org-ref-cite-onclick-minibuffer-menu
+
 *** A function to format a cite link
 
 Next, we define a formatting function for the cite link. This is done so that the cite link definition is very short, and easy to change. You just need to specify the functions in the definition. This function is deprecated. The formatting is defined later automatically.
@@ -1596,23 +2067,23 @@ Finally, we define the cite link. This is deprecated; the links are autogenerate
 #+END_SRC
 
 *** Automatic definition of the cite links
-There are many different kinds of citations in LaTeX, but they are all variants of a basic syntax of \citetype[optional text]{label1,label2}. Here we use lisp to generate the link definitions. We define a function that creates the code to create the link, and then we evaluate it. We also create the completion function for the new link, and add it to the list of known links. 
+There are many different kinds of citations in LaTeX, but they are all variants of a basic syntax of \citetype[optional text]{label1,label2}. Here we use lisp to generate the link definitions. We define a function that creates the code to create the link, and then we evaluate it. We also create the completion function for the new link, and add it to the list of known links.
 
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el 
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
 (defmacro org-ref-make-completion-function (type)
   `(defun ,(intern (format "org-%s-complete-link" type)) (&optional arg)
      (interactive)
-     (format "%s:%s" 
+     (format "%s:%s"
             ,type
-            (completing-read 
-             "bibtex key: " 
+            (completing-read
+             "bibtex key: "
              (let ((bibtex-files (org-ref-find-bibliography)))
                (bibtex-global-key-alist))))))
 #+END_SRC
 
 We will want to generate formatting functions for each citation type. The reason for doing this is so we can on the fly change the formatting later.
 
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el 
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
 (defmacro org-ref-make-format-function (type)
   `(defun ,(intern (format "org-ref-format-%s" type)) (keyword desc format)
      (cond
@@ -1628,10 +2099,10 @@ We will want to generate formatting functions for each citation type. The reason
                (lambda (key)
                  (format "%s" key))
                (org-ref-split-and-strip-string keyword) ",") "]"))
-       
-      ((eq format 'html) 
-       (mapconcat 
-       (lambda (key) 
+
+      ((eq format 'html)
+       (mapconcat
+       (lambda (key)
          (format "<a href=\"#%s\">%s</a>" key key))
        (org-ref-split-and-strip-string keyword) ","))
 
@@ -1643,12 +2114,30 @@ We will want to generate formatting functions for each citation type. The reason
         ;; bibtex format
        (concat "\\" ,type (when desc (org-ref-format-citation-description desc)) "{"
               (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
-              "}"))))))
-#+END_SRC
-
-
-
-We create the links by mapping the function onto the list of defined link types. 
+              "}")))
+      ;; 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
+
+
+
+We create the links by mapping the function onto the list of defined link types.
 
 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
 (defun org-ref-format-citation-description (desc)
@@ -1661,22 +2150,22 @@ We create the links by mapping the function onto the list of defined link types.
 
 (defun org-ref-define-citation-link (type &optional key)
   "add a citation link for org-ref. With optional key, set the reftex binding. For example:
-(org-ref-define-citation-link \"citez\" ?z) will create a new citez link, with reftex key of z, 
+(org-ref-define-citation-link \"citez\" ?z) will create a new citez link, with reftex key of z,
 and the completion function."
   (interactive "sCitation Type: \ncKey: ")
 
   ;; create the formatting function
   (eval `(org-ref-make-format-function ,type))
 
-  (eval-expression 
-   `(org-add-link-type 
+  (eval-expression
+   `(org-add-link-type
      ,type
-     'org-ref-cite-onclick-minibuffer-menu
+     org-ref-cite-onclick-function
      (quote ,(intern (format "org-ref-format-%s" type)))))
 
   ;; create the completion function
   (eval `(org-ref-make-completion-function ,type))
-  
+
   ;; store new type so it works with adding citations, which checks
   ;; for existence in this list
   (add-to-list 'org-ref-cite-types type)
@@ -1684,7 +2173,7 @@ and the completion function."
   ;; and finally if a key is specified, we modify the reftex menu
   (when key
     (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
-         (append (nth 2 (assoc 'org reftex-cite-format-builtin)) 
+         (append (nth 2 (assoc 'org reftex-cite-format-builtin))
                  `((,key  . ,(concat type ":%l")))))))
 
 ;; create all the link types and their completion functions
@@ -1704,39 +2193,41 @@ inserted. Use a prefix arg to get a menu of citation types."
   (let* ((object (org-element-context))
         (link-string-beginning (org-element-property :begin object))
         (link-string-end (org-element-property :end object))
-        (path (org-element-property :path object)))  
+        (path (org-element-property :path object)))
 
     (if (not alternative-cite)
-       
+
        (cond
         ;; case where we are in a link
-        ((and (equal (org-element-type object) 'link) 
+        ((and (equal (org-element-type object) 'link)
               (-contains? org-ref-cite-types (org-element-property :type object)))
          (goto-char link-string-end)
          ;; 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))  
+         (while (looking-back " ") (backward-char))
          (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
 
         ;; We are next to a link, and we want to append
-        ((save-excursion 
+        ((save-excursion
            (backward-char)
-           (and (equal (org-element-type (org-element-context)) 'link) 
+           (and (equal (org-element-type (org-element-context)) 'link)
                 (-contains? org-ref-cite-types (org-element-property :type (org-element-context)))))
-         (while (looking-back " ") (backward-char))  
+         (while (looking-back " ") (backward-char))
          (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
 
         ;; insert fresh link
-        (t 
-         (insert 
-          (concat org-ref-default-citation-link 
-                  ":" 
+        (t
+         (insert
+          (concat org-ref-default-citation-link
+                  ":"
                   (mapconcat 'identity (reftex-citation t) ",")))))
 
       ;; you pressed a C-u so we run this code
       (reftex-citation)))
   )
 #+END_SRC
+cite:zhou-2004-first-lda-u,paier-2006-errat,boes-2015-estim-bulk
+
 
 #+RESULTS:
 : org-ref-insert-cite-link
@@ -1747,10 +2238,10 @@ If you know the specific bibtex key, you may like to use completion directly. Yo
 #+BEGIN_SRC emacs-lisp  :tangle no
 (defun org-cite-complete-link (&optional arg)
   "Completion function for cite links"
-  (format "%s:%s" 
+  (format "%s:%s"
           org-ref-default-citation-link
-         (completing-read 
-          "bibtex key: " 
+         (completing-read
+          "bibtex key: "
           (let ((bibtex-files (org-ref-find-bibliography)))
             (bibtex-global-key-alist)))))
 #+END_SRC
@@ -1771,8 +2262,8 @@ org-mode already defines a store link function for bibtex entries. It does not s
 (defun org-ref-store-bibtex-entry-link ()
   "Save a citation link to the current bibtex entry. Saves in the default link type."
   (interactive)
-  (let ((link (concat org-ref-default-citation-link 
-                ":"   
+  (let ((link (concat org-ref-default-citation-link
+                ":"
                 (save-excursion
                   (bibtex-beginning-of-entry)
                   (reftex-get-bib-field "=key=" (bibtex-parse-entry))))))
@@ -1826,16 +2317,16 @@ index:encodings!input!cp850
 
      ;; get links
      (org-element-map (org-element-parse-buffer) 'link
-       (lambda (link)       
+       (lambda (link)
         (let ((type (nth 0 link))
               (plist (nth 1 link)))
-           
+
           (when (equal (plist-get plist ':type) "index")
             (add-to-list
-             '*index-links* 
+             '*index-links*
              (cons (plist-get plist :path)
                    (format
-                    "[[elisp:(progn (switch-to-buffer \"%s\") (goto-char %s))][%s]]"               
+                    "[[elisp:(progn (switch-to-buffer \"%s\") (goto-char %s))][%s]]"
 (current-buffer)
                     (plist-get plist :begin)  ;; position of link
                     ;; grab a description
@@ -1850,7 +2341,7 @@ index:encodings!input!cp850
 
      ;; sort the links
      (setq *index-links*  (cl-sort *index-links* 'string-lessp :key 'car))
-   
+
      ;; now first letters
      (dolist (link *index-links*)
        (add-to-list '*initial-letters* (substring (car link) 0 1) t))
@@ -1882,7 +2373,7 @@ index:encodings!input!cp850
 
 ** Glossary
 org-ref provides some minimal support for a glossary. See http://en.wikibooks.org/wiki/LaTeX/Glossary for details. You need to put these lines in the header.
+
 #+LATEX_HEADER: \usepackage{glossaries}
 #+LATEX_HEADER: \makeglossaries
 
@@ -1935,126 +2426,13 @@ And at the end of the document put \makeglossaries.
      (format "\\Glspl{%s}" path)))))
 #+END_SRC
 
-#+RESULTS:
-| Glspl             | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \Glspl{%s} path))))                                                                                                                                                                                                                                                                                                                     |
-| Gls               | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \Gls{%s} path))))                                                                                                                                                                                                                                                                                                                       |
-| glspl             | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \glspl{%s} path))))                                                                                                                                                                                                                                                                                                                     |
-| gls               | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \gls{%s} path))))                                                                                                                                                                                                                                                                                                                       |
-| newglossaryentry  | nil                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | (lambda (path desc format) (cond ((eq format (quote latex)) (format \newglossaryentry{%s}{%s} path desc))))                                                                                                                                                                                                                                                                                                 |
-| google            | (lambda (link-string) (browse-url (format http://www.google.com/search?q=%s (url-hexify-string link-string))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| ResearcherID      | (lambda (link-string) (browse-url (format http://www.researcherid.com/rid/%s link-string)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| orcid             | (lambda (link-string) (browse-url (format http://orcid.org/%s link-string)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| message           | org-mac-message-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| mac-outlook       | org-mac-outlook-message-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| skim              | org-mac-skim-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| addressbook       | org-mac-addressbook-item-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| x-together-item   | org-mac-together-item-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| ans               | (lambda (path) (let* ((fields (split-string path ::)) (label (nth 0 fields)) (data (nth 1 fields)) (data-file (format %s-%s.dat tq-userid label))) (let ((temp-file data-file) (temp-buffer (get-buffer-create (generate-new-buffer-name  *temp file*)))) (unwind-protect (prog1 (save-current-buffer (set-buffer temp-buffer) (insert data)) (save-current-buffer (set-buffer temp-buffer) (write-region nil nil temp-file nil 0))) (and (buffer-name temp-buffer) (kill-buffer temp-buffer)))) (mygit (format git add %s data-file)) (mygit (format git commit -m "%s" data-file)) (mygit git push origin master)))                                                                                                                                                                                              | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| mc                | (lambda (link) (org-entry-put (point) ANSWER link) (save-restriction (save-excursion (org-narrow-to-subtree) (goto-char (point-max)) (if (bolp) nil (insert \n)) (insert (format # you chose %s link)))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| exercise          | (lambda (arg) (tq-check-internet) (tq-get-assignment arg))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| solution          | (lambda (label) (tq-check-internet) (let ((default-directory (file-name-as-directory (expand-file-name tq-root-directory)))) (if (file-exists-p solutions) nil (make-directory solutions)) (let ((default-directory (file-name-as-directory (expand-file-name solutions)))) (if (file-exists-p label) (progn (find-file (concat label / label .org)) (tq-update)) (mygit (format git clone %s@%s:solutions/%s tq-current-course tq-git-server label)) (find-file (concat label / label .org))))))                                                                                                                                                                                                                                                                                                                  | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| assignment        | (lambda (arg) (tq-check-internet) (tq-get-assignment arg))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| doi               | doi-link-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| bibentry          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-bibentry                                                                                                                                                                                                                                                                                                                                                                                     |
-| Autocites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Autocites                                                                                                                                                                                                                                                                                                                                                                                    |
-| autocites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-autocites                                                                                                                                                                                                                                                                                                                                                                                    |
-| supercites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-supercites                                                                                                                                                                                                                                                                                                                                                                                   |
-| Textcites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Textcites                                                                                                                                                                                                                                                                                                                                                                                    |
-| textcites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-textcites                                                                                                                                                                                                                                                                                                                                                                                    |
-| Smartcites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Smartcites                                                                                                                                                                                                                                                                                                                                                                                   |
-| smartcites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-smartcites                                                                                                                                                                                                                                                                                                                                                                                   |
-| footcitetexts     | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcitetexts                                                                                                                                                                                                                                                                                                                                                                                |
-| footcites         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcites                                                                                                                                                                                                                                                                                                                                                                                    |
-| Parencites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Parencites                                                                                                                                                                                                                                                                                                                                                                                   |
-| parencites        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-parencites                                                                                                                                                                                                                                                                                                                                                                                   |
-| Cites             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Cites                                                                                                                                                                                                                                                                                                                                                                                        |
-| cites             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-cites                                                                                                                                                                                                                                                                                                                                                                                        |
-| fnotecite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-fnotecite                                                                                                                                                                                                                                                                                                                                                                                    |
-| Pnotecite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Pnotecite                                                                                                                                                                                                                                                                                                                                                                                    |
-| pnotecite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-pnotecite                                                                                                                                                                                                                                                                                                                                                                                    |
-| Notecite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Notecite                                                                                                                                                                                                                                                                                                                                                                                     |
-| notecite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-notecite                                                                                                                                                                                                                                                                                                                                                                                     |
-| footfullcite      | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footfullcite                                                                                                                                                                                                                                                                                                                                                                                 |
-| fullcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-fullcite                                                                                                                                                                                                                                                                                                                                                                                     |
-| citeurl           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeurl                                                                                                                                                                                                                                                                                                                                                                                      |
-| citedate*         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citedate*                                                                                                                                                                                                                                                                                                                                                                                    |
-| citedate          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citedate                                                                                                                                                                                                                                                                                                                                                                                     |
-| citetitle*        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citetitle*                                                                                                                                                                                                                                                                                                                                                                                   |
-| citetitle         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citetitle                                                                                                                                                                                                                                                                                                                                                                                    |
-| Citeauthor*       | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citeauthor*                                                                                                                                                                                                                                                                                                                                                                                  |
-| Autocite*         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Autocite*                                                                                                                                                                                                                                                                                                                                                                                    |
-| autocite*         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-autocite*                                                                                                                                                                                                                                                                                                                                                                                    |
-| Autocite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Autocite                                                                                                                                                                                                                                                                                                                                                                                     |
-| autocite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-autocite                                                                                                                                                                                                                                                                                                                                                                                     |
-| supercite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-supercite                                                                                                                                                                                                                                                                                                                                                                                    |
-| parencite*        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-parencite*                                                                                                                                                                                                                                                                                                                                                                                   |
-| cite*             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-cite*                                                                                                                                                                                                                                                                                                                                                                                        |
-| Smartcite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Smartcite                                                                                                                                                                                                                                                                                                                                                                                    |
-| smartcite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-smartcite                                                                                                                                                                                                                                                                                                                                                                                    |
-| Textcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Textcite                                                                                                                                                                                                                                                                                                                                                                                     |
-| textcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-textcite                                                                                                                                                                                                                                                                                                                                                                                     |
-| footcitetext      | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcitetext                                                                                                                                                                                                                                                                                                                                                                                 |
-| footcite          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-footcite                                                                                                                                                                                                                                                                                                                                                                                     |
-| Parencite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Parencite                                                                                                                                                                                                                                                                                                                                                                                    |
-| parencite         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-parencite                                                                                                                                                                                                                                                                                                                                                                                    |
-| Cite              | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Cite                                                                                                                                                                                                                                                                                                                                                                                         |
-| Citeauthor        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citeauthor                                                                                                                                                                                                                                                                                                                                                                                   |
-| Citealp           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citealp                                                                                                                                                                                                                                                                                                                                                                                      |
-| Citealt           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citealt                                                                                                                                                                                                                                                                                                                                                                                      |
-| Citep             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citep                                                                                                                                                                                                                                                                                                                                                                                        |
-| Citet             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-Citet                                                                                                                                                                                                                                                                                                                                                                                        |
-| citeyear*         | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeyear*                                                                                                                                                                                                                                                                                                                                                                                    |
-| citeyear          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeyear                                                                                                                                                                                                                                                                                                                                                                                     |
-| citeauthor*       | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeauthor*                                                                                                                                                                                                                                                                                                                                                                                  |
-| citeauthor        | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citeauthor                                                                                                                                                                                                                                                                                                                                                                                   |
-| citetext          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citetext                                                                                                                                                                                                                                                                                                                                                                                     |
-| citenum           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citenum                                                                                                                                                                                                                                                                                                                                                                                      |
-| citealp*          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citealp*                                                                                                                                                                                                                                                                                                                                                                                     |
-| citealp           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citealp                                                                                                                                                                                                                                                                                                                                                                                      |
-| citealt*          | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citealt*                                                                                                                                                                                                                                                                                                                                                                                     |
-| citealt           | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citealt                                                                                                                                                                                                                                                                                                                                                                                      |
-| citep*            | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citep*                                                                                                                                                                                                                                                                                                                                                                                       |
-| citep             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citep                                                                                                                                                                                                                                                                                                                                                                                        |
-| citet*            | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citet*                                                                                                                                                                                                                                                                                                                                                                                       |
-| citet             | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-citet                                                                                                                                                                                                                                                                                                                                                                                        |
-| nocite            | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-nocite                                                                                                                                                                                                                                                                                                                                                                                       |
-| cite              | org-ref-cite-onclick-minibuffer-menu                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | org-ref-format-cite                                                                                                                                                                                                                                                                                                                                                                                         |
-| eqref             | (lambda (label) on clicking goto the label. Navigate back with C-c & (org-mark-ring-push) (widen) (goto-char (point-min)) (if (or (re-search-forward (format label:%s label) nil t) (re-search-forward (format \label{%s} label) nil t) (re-search-forward (format ^#\+label:\s-*\(%s\)\b label) nil t)) nil (org-mark-ring-goto) (error %s not found label)) (message go back with (org-mark-ring-goto) `C-c &`))                                                                                                                                                                                                                                                                                                                                                                                                 | (lambda (keyword desc format) (cond ((eq format (quote html)) (format (<eqref>%s</eqref>) path)) ((eq format (quote latex)) (format \eqref{%s} keyword))))                                                                                                                                                                                                                                                  |
-| nameref           | (lambda (label) on clicking goto the label. Navigate back with C-c & (org-mark-ring-push) (widen) (if (or (progn (goto-char (point-min)) (re-search-forward (format \label{%s} label) nil t))) nil (org-mark-ring-goto) (error %s not found label)) (message go back with (org-mark-ring-goto) `C-c &`))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | (lambda (keyword desc format) (cond ((eq format (quote html)) (format (<nameref>%s</nameref>) path)) ((eq format (quote latex)) (format \nameref{%s} keyword))))                                                                                                                                                                                                                                            |
-| pageref           | (lambda (label) on clicking goto the label. Navigate back with C-c & (org-mark-ring-push) (widen) (if (or (progn (goto-char (point-min)) (re-search-forward (format label:%s\b label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format \label{%s} label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format ^#\+label:\s-*\(%s\)\b label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format ^#\+tblname:\s-*\(%s\)\b label) nil t))) nil (org-mark-ring-goto) (error %s not found label)) (message go back with (org-mark-ring-goto) `C-c &`))                                                                                                                                                                                                                     | (lambda (keyword desc format) (cond ((eq format (quote html)) (format (<pageref>%s</pageref>) path)) ((eq format (quote latex)) (format \pageref{%s} keyword))))                                                                                                                                                                                                                                            |
-| ref               | (lambda (label) on clicking goto the label. Navigate back with C-c & (org-mark-ring-push) (widen) (if (or (progn (goto-char (point-min)) (re-search-forward (format label:%s\b label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format \label{%s} label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format ^#\+label:\s-*\(%s\)\b label) nil t)) (progn (goto-char (point-min)) (re-search-forward (format ^#\+tblname:\s-*\(%s\)\b label) nil t))) nil (org-mark-ring-goto) (error %s not found label)) (org-show-entry) (message go back with (org-mark-ring-goto) `C-c &`))                                                                                                                                                                                                    | (lambda (keyword desc format) (cond ((eq format (quote html)) (format (<ref>%s</ref>) path)) ((eq format (quote latex)) (format \ref{%s} keyword))))                                                                                                                                                                                                                                                        |
-| 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 (+ (count-matches (format label:%s\b[^-:] label) (point-min) (point-max) t) (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 ^#\+label:\s-*%s\b[^-:] label) (point-min) (point-max) t)))))                                                                                                                                                                                                                                                                                                                           | (lambda (keyword desc format) (cond ((eq format (quote html)) (format (<label>%s</label>) path)) ((eq format (quote latex)) (format \label{%s} keyword))))                                                                                                                                                                                                                                                  |
-| list-of-tables    | org-ref-list-of-tables                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             | (lambda (keyword desc format) (cond ((eq format (quote latex)) (format \listoftables))))                                                                                                                                                                                                                                                                                                                    |
-| list-of-figures   | org-ref-list-of-figures                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | (lambda (keyword desc format) (cond ((eq format (quote latex)) (format \listoffigures))))                                                                                                                                                                                                                                                                                                                   |
-| addbibresource    | (lambda (link-string) (let* ((bibfile) (object (org-element-context)) (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))) (set (make-local-variable (quote reftex-default-addbibresource)) (split-string (org-element-property :path object) ,)) (save-excursion (if (search-forward , link-string-end 1 1) (setq key-end (- (match-end 0) 1)) (setq key-end (point)))) (save-excursion (if (search-backward , link-string-beginning 1 1) (setq key-beginning (+ (match-beginning 0) 1)) (setq key-beginning (point)))) (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end))) (find-file bibfile))) | (lambda (keyword desc format) (cond ((eq format (quote html)) (format )) ((eq format (quote latex)) (format \addbibresource{%s} keyword))))                                                                                                                                                                                                                                                                 |
-| bibliographystyle | (lambda (arg) (message Nothing implemented for clicking here.))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | (lambda (keyword desc format) (cond ((eq format (quote latex)) (format \bibliographystyle{%s} keyword))))                                                                                                                                                                                                                                                                                                   |
-| printbibliography | (lambda (arg) (message Nothing implemented for clicking here.))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | (lambda (keyword desc format) (cond ((eq format (quote org)) (org-ref-get-org-bibliography)) ((eq format (quote html)) (org-ref-get-html-bibliography)) ((eq format (quote latex)) \printbibliography)))                                                                                                                                                                                                    |
-| nobibliography    | (lambda (link-string) (let* ((bibfile) (object (org-element-context)) (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))) (set (make-local-variable (quote reftex-default-bibliography)) (split-string (org-element-property :path object) ,)) (save-excursion (if (search-forward , link-string-end 1 1) (setq key-end (- (match-end 0) 1)) (setq key-end (point)))) (save-excursion (if (search-backward , link-string-beginning 1 1) (setq key-beginning (+ (match-beginning 0) 1)) (setq key-beginning (point)))) (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end))) (find-file bibfile)))   | (lambda (keyword desc format) (cond ((eq format (quote org)) (org-ref-get-org-bibliography)) ((eq format (quote ascii)) (org-ref-get-ascii-bibliography)) ((eq format (quote html)) (org-ref-get-html-bibliography)) ((eq format (quote latex)) (format \nobibliography{%s} (replace-regexp-in-string \.bib  (mapconcat (quote identity) (mapcar (quote expand-file-name) (split-string keyword ,)) ,)))))) |
-| bibliography      | (lambda (link-string) (let* ((bibfile) (object (org-element-context)) (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))) (set (make-local-variable (quote reftex-default-bibliography)) (split-string (org-element-property :path object) ,)) (save-excursion (if (search-forward , link-string-end 1 1) (setq key-end (- (match-end 0) 1)) (setq key-end (point)))) (save-excursion (if (search-backward , link-string-beginning 1 1) (setq key-beginning (+ (match-beginning 0) 1)) (setq key-beginning (point)))) (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end))) (find-file bibfile)))   | (lambda (keyword desc format) (cond ((eq format (quote org)) (org-ref-get-org-bibliography)) ((eq format (quote ascii)) (org-ref-get-ascii-bibliography)) ((eq format (quote html)) (org-ref-get-html-bibliography)) ((eq format (quote latex)) (format \bibliography{%s} (replace-regexp-in-string \.bib  (mapconcat (quote identity) (mapcar (quote expand-file-name) (split-string keyword ,)) ,))))))   |
-| rmail             | org-rmail-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| mhe               | org-mhe-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| irc               | org-irc-visit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| info              | org-info-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| gnus              | org-gnus-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| docview           | org-docview-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | org-docview-export                                                                                                                                                                                                                                                                                                                                                                                          |
-| bibtex            | org-bibtex-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| bbdb              | org-bbdb-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | org-bbdb-export                                                                                                                                                                                                                                                                                                                                                                                             |
-| pydoc             | (lambda (link-string) (shell-command (format python -m pydoc %s link-string)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| index             | (lambda (path) (tq-index) (occur path))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| attachfile        | (lambda (link-string) (org-open-file link-string))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 | (lambda (keyword desc format) (cond ((eq format (quote html)) (format )) ((eq format (quote latex)) (format \attachfile{%s} keyword))))                                                                                                                                                                                                                                                                     |
-| msx               | org-msx-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| id                | org-id-open                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| file+emacs        | org-open-file-with-emacs                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-| file+sys          | org-open-file-with-system                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | nil                                                                                                                                                                                                                                                                                                                                                                                                         |
-
-
-
 * Utilities
 ** create simple text citation from bibtex entry
 
 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
 (defun org-ref-bib-citation ()
-  "from a bibtex entry, create and return a simple citation string."
+  "From a bibtex entry, create and return a simple citation string.
+This assumes you are in an article."
 
   (bibtex-beginning-of-entry)
   (let* ((cb (current-buffer))
@@ -2161,17 +2539,17 @@ construct the heading by hand."
     (with-temp-buffer
       (insert key)
       (kill-ring-save (point-min) (point-max)))
-    
+
     ;; now look for entry in the notes file
     (if  org-ref-bibliography-notes
        (find-file-other-window org-ref-bibliography-notes)
       (error "org-ref-bib-bibliography-notes is not set to anything"))
-    
+
     (goto-char (point-min))
     ;; put new entry in notes if we don't find it.
     (if (re-search-forward (format ":Custom_ID: %s$" key) nil 'end)
        (funcall org-ref-open-notes-function)
-      ;; no entry found, so add one    
+      ;; no entry found, so add one
       (insert (format "\n** TODO %s - %s" year title))
       (insert (format"
  :PROPERTIES:
@@ -2199,9 +2577,9 @@ key author journal year volume pages doi url key org-ref-pdf-directory key))
     (if  org-ref-bibliography-notes
        (find-file-other-window org-ref-bibliography-notes)
       (error "org-ref-bib-bibliography-notes is not set to anything"))
-    
+
     (goto-char (point-min))
-    
+
     (re-search-forward (format
                        ":Custom_ID: %s$"
                        (first (reftex-citation t)) nil 'end))
@@ -2258,13 +2636,13 @@ Relies on the python script /upload_bibtex_citeulike.py being in the user direct
 #+END_SRC
 
 *** The upload script
-Here is the python script for uploading. 
+Here is the python script for uploading.
 
 *************** 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
 
@@ -2321,7 +2699,7 @@ print r
     (shell-command (concat "pdflatex " bib-base))
     (kill-buffer texfile)
     (org-open-file pdffile)
-    )) 
+    ))
 #+END_SRC
 
 ** Extract bibtex entries cited in an org-file
@@ -2338,20 +2716,20 @@ If no bibliography is in the buffer the `reftex-default-bibliography' is used."
          (contents (buffer-string))
          (cb (current-buffer))
         basename texfile bibfile results)
-    
+
     ;; open tempfile and insert org-buffer contents
     (find-file tempname)
     (insert contents)
-    (setq basename (file-name-sans-extension 
+    (setq basename (file-name-sans-extension
                    (file-name-nondirectory buffer-file-name))
          texfile (concat tempname ".tex")
          bibfile (concat tempname ".bib"))
-    
+
     ;; see if we have a bibliography, and insert the default one if not.
     (save-excursion
       (goto-char (point-min))
       (unless (re-search-forward "^bibliography:" (point-max) 'end)
-       (insert (format "\nbibliography:%s" 
+       (insert (format "\nbibliography:%s"
                        (mapconcat 'identity reftex-default-bibliography ",")))))
     (save-buffer)
 
@@ -2388,6 +2766,9 @@ If no bibliography is in the buffer the `reftex-default-bibliography' is used."
 #+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
@@ -2399,7 +2780,7 @@ Depending on how you enter citations, you may have citations with no correspondi
        (found nil))
     (dolist (arg list i)
       (if (string-match (concat "^" substring "$") arg)
-         (progn 
+         (progn
            (setq found t)
            (return i)))
       (setq i (+ i 1)))
@@ -2419,15 +2800,23 @@ Makes a new buffer with clickable links."
         (bad-citations '()))
 
     (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)) )
+      (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))
-               (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
@@ -2445,8 +2834,164 @@ Makes a new buffer with clickable links."
       (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. 
+I like my bibtex files to be 100% ascii. This function finds the non-ascii characters so you can replace them.
 
 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
 (defun org-ref-find-non-ascii-characters ()
@@ -2481,16 +3026,16 @@ I like neat and orderly bibtex entries.That means the fields are in a standard o
 
     (cond
      ;; right now we only resort articles
-     ((string= (downcase type) "article") 
+     ((string= (downcase type) "article")
       (bibtex-kill-entry)
       (insert
-       (concat "@article{" key ",\n" 
-              (mapconcat  
-               (lambda (field) 
+       (concat "@article{" key ",\n"
+              (mapconcat
+               (lambda (field)
                  (when (member field entry-fields)
                    (format "%s = %s," (downcase field) (cdr (assoc field entry))))) master "\n")
-              (mapconcat 
-               (lambda (field) 
+              (mapconcat
+               (lambda (field)
                  (format "%s = %s," (downcase field) (cdr (assoc field entry)))) other-fields "\n")
               "\n}\n\n"))
       (bibtex-find-entry key)
@@ -2506,7 +3051,7 @@ see [[file:emacs-24.3/lisp/textmodes/bibtex.el::bibtex-autokey-before-presentati
 (defun org-ref-clean-bibtex-entry(&optional keep-key)
   "clean and replace the key in a bibtex function. When keep-key is t, do not replace it. You can use a prefix to specify the key should be kept"
   (interactive "P")
-  (bibtex-beginning-of-entry) 
+  (bibtex-beginning-of-entry)
 (end-of-line)
   ;; some entries do not have a key or comma in first line. We check and add it, if needed.
   (unless (string-match ",$" (thing-at-point 'line))
@@ -2533,7 +3078,7 @@ see [[file:emacs-24.3/lisp/textmodes/bibtex.el::bibtex-autokey-before-presentati
 
     ;; asap articles often set year to 0, which messes up key
     ;; generation. fix that.
-    (when (string= "0" year)  
+    (when (string= "0" year)
       (bibtex-beginning-of-entry)
       (goto-char (car (cdr (bibtex-search-forward-field "year" t))))
       (bibtex-kill-field)
@@ -2543,7 +3088,7 @@ see [[file:emacs-24.3/lisp/textmodes/bibtex.el::bibtex-autokey-before-presentati
 
     ;; fix pages if they are empty if there is an eid to put there.
     (when (string= "-" pages)
-      (when eid          
+      (when eid
        (bibtex-beginning-of-entry)
        ;; this seems like a clunky way to set the pages field.But I
        ;; cannot find a better way.
@@ -2582,7 +3127,7 @@ see [[file:emacs-24.3/lisp/textmodes/bibtex.el::bibtex-autokey-before-presentati
          (setq key (bibtex-read-key "Duplicate Key found, edit: " key)))
 
        (insert key)
-       (kill-new key))) ;; save key for pasting            
+       (kill-new key))) ;; save key for pasting
 
     ;; run hooks. each of these operates on the entry with no arguments.
     ;; this did not work like  i thought, it gives a symbolp error.
@@ -2592,7 +3137,7 @@ see [[file:emacs-24.3/lisp/textmodes/bibtex.el::bibtex-autokey-before-presentati
                (save-excursion
                  (funcall x))))
            org-ref-clean-bibtex-entry-hook)
-    
+
     ;; sort fields within entry
     (org-ref-sort-bibtex-entry)
     ;; check for non-ascii characters
@@ -2621,14 +3166,14 @@ I prefer citations in chronological order within a grouping. These functions sor
 (defun org-ref-sort-citation-link ()
  "replace link at point with sorted link by year"
  (interactive)
- (let* ((object (org-element-context))  
+ (let* ((object (org-element-context))
         (type (org-element-property :type object))
        (begin (org-element-property :begin object))
        (end (org-element-property :end object))
        (link-string (org-element-property :path object))
        keys years data)
   (setq keys (org-ref-split-and-strip-string link-string))
-  (setq years (mapcar 'org-ref-get-citation-year keys)) 
+  (setq years (mapcar 'org-ref-get-citation-year keys))
   (setq data (mapcar* (lambda (a b) `(,a . ,b)) years keys))
   (setq data (cl-sort data (lambda (x y) (< (string-to-int (car x)) (string-to-int (car y))))))
   ;; now get the keys separated by commas
@@ -2650,7 +3195,7 @@ Sometimes it may be helpful to manually change the order of citations. These fun
 (defun org-ref-swap-citation-link (direction)
  "move citation at point in direction +1 is to the right, -1 to the left"
  (interactive)
- (let* ((object (org-element-context))  
+ (let* ((object (org-element-context))
         (type (org-element-property :type object))
        (begin (org-element-property :begin object))
        (end (org-element-property :end object))
@@ -2663,18 +3208,163 @@ Sometimes it may be helpful to manually change the order of citations. These fun
         (setq i (index key keys))  ;; defined in org-ref
        (if (> direction 0) ;; shift right
            (org-ref-swap-keys i (+ i 1) keys)
-         (org-ref-swap-keys i (- i 1) keys))   
+         (org-ref-swap-keys i (- i 1) keys))
        (setq keys (mapconcat 'identity keys ","))
        ;; and replace the link with the sorted keys
        (cl--set-buffer-substring begin end (concat type ":" keys " "))
        ;; now go forward to key so we can move with the key
-       (re-search-forward key) 
+       (re-search-forward key)
        (goto-char (match-beginning 0)))))
 
 ;; add hooks to make it work
 (add-hook 'org-shiftright-hook (lambda () (org-ref-swap-citation-link 1)))
 (add-hook 'org-shiftleft-hook (lambda () (org-ref-swap-citation-link -1)))
 #+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 run this in an idle timer.
+
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(defun org-ref-get-label-context (label)
+  "Return a string of context around a label."
+  (save-excursion
+    (catch 'result
+      (goto-char (point-min))
+      (when (re-search-forward
+            (format "label:%s\\b" label) nil t)
+       (throw 'result (buffer-substring
+                       (progn
+                         (previous-line)
+                         (beginning-of-line)
+                         (point))
+                       (progn
+                         (forward-line 4)
+                         (point)))))
+
+      (goto-char (point-min))
+      (when (re-search-forward
+            (format "\\label{%s}" label) nil t)
+       (throw 'result (buffer-substring
+                       (progn
+                         (previous-line)
+                         (beginning-of-line)
+                         (point))
+                       (progn
+                         (forward-line 4)
+                         (point)))))
+
+      (goto-char (point-min))
+      (when (re-search-forward
+            (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t)
+       (throw 'result (buffer-substring
+                       (progn
+                         (previous-line)
+                         (beginning-of-line)
+                         (point))
+                       (progn
+                         (forward-line 4)
+                         (point)))))
+
+      (goto-char (point-min))
+      (when (re-search-forward
+            (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t)
+       (throw 'result (buffer-substring
+                       (progn
+                         (previous-line)
+                         (beginning-of-line)
+                         (point))
+                       (progn
+                         (forward-line 4)
+                         (point)))))
+      (throw 'result "!!! NO CONTEXT FOUND !!!"))))
+
+
+(defun org-ref-link-message ()
+  "Print a minibuffer message about the link that point is on."
+  (interactive)
+  (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