X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=org-ref.org;h=90863161b12d4ceb30e285b8b29c214e3532c42a;hb=a6b2a0401a36d31acf8faa579f0c27cfc22f2a5c;hp=71dff79ece61eaddbd83571e0ddac3e8d4c8cce2;hpb=7d5790254b19acec7dc688054a65790808bf733f;p=org-ref.git
diff --git a/org-ref.org b/org-ref.org
index 71dff79..9086316 100644
--- a/org-ref.org
+++ b/org-ref.org
@@ -7,7 +7,7 @@
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
@@ -38,11 +38,11 @@ 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 +51,8 @@ The only external require is reftex-cite
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(require 'reftex-cite)
(require 'dash)
+(require 'helm)
+(require 'helm-bibtex)
#+END_SRC
** Custom variables
@@ -103,6 +105,46 @@ There are some variables needed later to tell this library where you store your
"string to format an entry. Just the reference, no numbering at the beginning, etc... see the `org-ref-reftex-format-citation' docstring for the escape codes."
:type 'string
:group 'org-ref)
+
+(defcustom org-ref-open-notes-function
+ (lambda ()
+ (org-show-entry)
+ (show-branches)
+ (show-children)
+ (org-cycle '(64))
+ ;;(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"
+: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.
@@ -140,6 +182,8 @@ This next variable determines the citation types that are available in org-ref.
"footcites" "footcitetexts"
"smartcites" "Smartcites" "textcites" "Textcites"
"supercites" "autocites" "Autocites"
+ ;; for the bibentry package
+ "bibentry"
)
"List of citation types known in org-ref"
:type '(repeat :tag "List of citation types" string)
@@ -166,15 +210,19 @@ We need a hook variable to store user-defined bibtex entry cleaning functions
We setup reftex here. We use a custom insert cite link function defined here: [[*org-ref-insert-cite-link][org-ref-insert-cite-link]]. We setup reftex to use our org citation format.
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(require 'reftex)
(defun org-mode-reftex-setup ()
- (load-library "reftex")
(and (buffer-file-name)
(file-exists-p (buffer-file-name))
(global-auto-revert-mode t)
- (reftex-parse-all))
+ ;; 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)
+ )
(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))
+ (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)
@@ -197,7 +245,7 @@ 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
@@ -246,7 +294,7 @@ 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)
@@ -363,7 +411,7 @@ 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))))))
@@ -377,7 +425,7 @@ 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
@@ -402,11 +450,11 @@ This code provides some functions to generate a simple sorted bibliography in ht
"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)))))))))
@@ -426,7 +474,7 @@ 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)))
@@ -451,7 +499,7 @@ 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))))))
@@ -474,7 +522,7 @@ 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)))
@@ -498,12 +546,12 @@ 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
=============
"
@@ -520,15 +568,83 @@ 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-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)))
+
+ ;; We set the reftex-default-bibliography
+ ;; 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)
+ (split-string (org-element-property :path object) ","))
+
+ ;; now if we have comma separated bibliographies
+ ;; we find the one clicked on. we want to
+ ;; search forward to next comma from point
+ (save-excursion
+ (if (search-forward "," link-string-end 1 1)
+ (setq key-end (- (match-end 0) 1)) ; we found a match
+ (setq key-end (point)))) ; no comma found so take the point
+ ;; and backward to previous comma from point
+ (save-excursion
+ (if (search-backward "," link-string-beginning 1 1)
+ (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
+ (setq key-beginning (point)))) ; no match found
+ ;; save the key we clicked on.
+ (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
+ (find-file bibfile))) ; open file on click
+
+ ;; formatting code
+ (lambda (keyword desc format)
+ (cond
+ ((eq format 'org) (org-ref-get-org-bibliography))
+ ((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
+ (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.
+
+#+BEGIN_LaTeX
+ \input{project-description.bbl}
+#+END_LaTeX
+
+Here, we make a =nobibliography= link that acts like the bibliography, enables creation of the bbl file, but does not put an actual bibliography in the file.
+
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(org-add-link-type "nobibliography"
+ ;; 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)
;; 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
@@ -541,7 +657,7 @@ 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
@@ -567,8 +683,21 @@ 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
- (format "\\bibliography{%s}" (replace-regexp-in-string "\\.bib" "" (expand-file-name keyword)))))))
+ ;; write out the latex bibliography command
+
+; (format "{\\setbox0\\vbox{\\bibliography{%s}}}"
+; (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
+; (mapcar 'expand-file-name
+; (split-string keyword ","))
+; ",")))
+
+ (format "\\nobibliography{%s}"
+ (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
+ (mapcar 'expand-file-name
+ (split-string keyword ","))
+ ",")))
+
+ ))))
#+END_SRC
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
@@ -597,7 +726,7 @@ 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)
@@ -616,15 +745,15 @@ 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
@@ -637,7 +766,7 @@ 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
@@ -676,27 +805,27 @@ 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)
@@ -707,7 +836,7 @@ 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)
@@ -726,20 +855,20 @@ 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)
@@ -750,7 +879,7 @@ 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)
@@ -765,18 +894,21 @@ The label link provides a way to create labels in org-mode. We make it clickable
*************** END
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+
+(defun org-ref-count-labels (label)
+ (+ (count-matches (format "label:%s\\b[^-:]" label) (point-min) (point-max) t)
+ ;; 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)))
+
(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)))))
+ (message (format "%s occurences" (org-ref-count-labels label))))
(lambda (keyword desc format)
(cond
((eq format 'html) (format "()" path))
@@ -789,9 +921,9 @@ 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"
@@ -823,7 +955,7 @@ 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.
@@ -841,7 +973,7 @@ 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))
@@ -854,7 +986,7 @@ 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))
@@ -870,6 +1002,7 @@ At the moment, ref links are not usable for section links. You need [[#CUSTOM_ID
;; we did not find anything, so go back to where we came
(org-mark-ring-goto)
(error "%s not found" label))
+ (org-show-entry)
(message "go back with (org-mark-ring-goto) `C-c &`"))
;formatting
(lambda (keyword desc format)
@@ -879,14 +1012,25 @@ At the moment, ref links are not usable for section links. You need [[#CUSTOM_ID
(format "\\ref{%s}" keyword)))))
#+END_SRC
-It would be nice to use completion to enter a ref link, where a list of labels is provided. The following code searches the buffer for labels, custom_ids, and table names as potential items to make a ref link to.
+It would be nice to use completion to enter a ref link, where a list of labels is provided. The following code searches the buffer for org and latex labels, custom_ids, and table names as potential items to make a ref link to.
+
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(defun org-ref-get-org-labels ()
+ "find #+LABEL: labels"
+ (save-excursion
+ (goto-char (point-min))
+ (let ((matches '()))
+ (while (re-search-forward "^#\\+label:\\s-+\\(.*\\)\\b" (point-max) t)
+ (add-to-list 'matches (match-string-no-properties 1) t))
+matches)))
+#+END_SRC
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-ref-get-custom-ids ()
"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)))))))
@@ -896,7 +1040,7 @@ results))
Here we get a list of the labels defined as raw latex labels, e.g. \label{eqtre}.
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-ref-get-latex-labels ()
-(save-excursion
+ (save-excursion
(goto-char (point-min))
(let ((matches '()))
(while (re-search-forward "\\\\label{\\([a-zA-z0-9:-]*\\)}" (point-max) t)
@@ -909,7 +1053,7 @@ Finally, we get the table names.
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-ref-get-tblnames ()
(org-element-map (org-element-parse-buffer 'element) 'table
- (lambda (table)
+ (lambda (table)
(org-element-property :name table))))
#+END_SRC
@@ -925,7 +1069,7 @@ Now, we can put all the labels together which will give us a list of candidates.
(let ((matches '()))
(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-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.
@@ -961,7 +1105,7 @@ 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))
@@ -974,7 +1118,7 @@ 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))
@@ -1048,7 +1192,7 @@ 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"
@@ -1078,7 +1222,6 @@ This is just the LaTeX ref for equations. On export, the reference is enclosed i
(format "\\eqref{%s}" keyword)))))
#+END_SRC
-
** cite
This is the main reason this library exists. We want the following behavior. A cite link should be able to contain multiple bibtex keys. You should be able to click on the link, and get a brief citation of the entry for that key, and a menu of options to open the bibtex file, open a pdf if you have it, open your notes on the entry, or open a url if it exists. You should be able to insert new references onto an existing cite link, or create new ones easily. The following code implements these features.
@@ -1094,10 +1237,8 @@ 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)))
- (message "%s" 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.
(let ((cp (point)))
@@ -1107,10 +1248,10 @@ 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))
@@ -1159,14 +1300,14 @@ 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))
@@ -1177,7 +1318,7 @@ 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)))
@@ -1187,7 +1328,7 @@ 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)
@@ -1210,67 +1351,11 @@ 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
-**** Creating the menu for when we click on a key
- :PROPERTIES:
- :ID: d7b7530b-802f-42b1-b61e-1e77da33e278
- :END:
-When we click on a cite link, we want to get a menu in the minibuffer. We need to create a string for this. We want a citation, and some options that depend on the key. We want to know if the key is found, if there is a pdf, if etc... Here we create that string.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-get-menu-options ()
- "returns a dynamically determined string of options for the citation under point.
-
-we check to see if there is pdf, and if the key actually exists in the bibliography"
- (interactive)
- (let* ((results (org-ref-get-bibtex-key-and-file))
- (key (car results))
- (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
- (bibfile (cdr results))
- m1 m2 m3 m4 m5 menu-string)
- (setq m1 (if bibfile
- "(o)pen"
- "(No key found)"))
-
- (setq m3 (if (file-exists-p pdf-file)
- "(p)df"
- "(No pdf found)"))
-
- (setq m4 (if (not
- (and bibfile
- (string= (catch 'url
- (progn
-
- (with-temp-buffer
- (insert-file-contents bibfile)
- (bibtex-search-entry key)
- (when (not
- (string= (setq url (bibtex-autokey-get-field "url")) ""))
- (throw 'url url))
-
- (when (not
- (string= (setq url (bibtex-autokey-get-field "doi")) ""))
- (throw 'url url))))) "")))
- "(u)rl" "(no url found)"))
- (setq m5 "(n)otes")
- (setq m2 (if bibfile
- (progn
- (setq citation (progn
- (with-temp-buffer
- (insert-file-contents bibfile)
- (bibtex-search-entry key)
- (org-ref-bib-citation))))
- citation)
- "no key found"))
-
- (setq menu-string (mapconcat 'identity (list m2 "\n" m1 m3 m4 m5 "(q)uit") " "))
- menu-string))
-#+END_SRC
-
**** convenience functions to act on citation at point
:PROPERTIES:
:ID: af0b2a82-a7c9-4c08-9dac-09f93abc4a92
@@ -1314,6 +1399,7 @@ We need some convenience functions to open act on the citation at point. These w
(browse-url (format "http://dx.doi.org/%s" doi)))
(throw 'done nil))))))))
+
(defun org-ref-open-notes-at-point ()
"open the notes for bibtex key under point."
(interactive)
@@ -1326,19 +1412,21 @@ We need some convenience functions to open act on the citation at point. These w
(bibtex-search-entry key)
(org-ref-open-bibtex-notes)))))
+
(defun org-ref-citation-at-point ()
"give message of current citation at point"
(interactive)
(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)
(bibtex-search-entry key)
(org-ref-bib-citation))))))
+
(defun org-ref-open-citation-at-point ()
"open bibtex file to key at point"
(interactive)
@@ -1351,56 +1439,223 @@ We need some convenience functions to open act on the citation at point. These w
#+END_SRC
**** the actual minibuffer menu
-Now, we create the 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
-(defun org-ref-cite-onclick-minibuffer-menu (&optional link-string)
- "use a minibuffer to select options for the citation under point.
+#+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).
+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)
+ ("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.")
-you select your option with a single key press."
+
+(defun org-ref-copy-entry-as-summary ()
+ "Copy the bibtex entry for the citation at point as a summary."
(interactive)
- (let* ((choice (read-char (org-ref-get-menu-options)))
- (results (org-ref-get-bibtex-key-and-file))
+ (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))
- (cb (current-buffer))
- (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
- (bibfile (cdr results)))
+ (bibfile (cdr results))
+ doi)
+ (save-excursion
+ (with-temp-buffer
+ (insert-file-contents bibfile)
+ (bibtex-search-entry key)
+ (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 ()
+ "open the doi in wos for bibtex key under point."
+ (interactive)
+ (doi-utils-wos (org-ref-get-doi-at-point)))
- (cond
- ;; open
- ((= choice ?o)
- (find-file bibfile)
- (bibtex-search-entry key))
- ;; cite
- ((= choice ?c)
- (org-ref-citation-at-point))
-
+(defun org-ref-wos-citing-at-point ()
+ "open the doi in wos citing articles for bibtex key under point."
+ (interactive)
+ (doi-utils-wos-citing (org-ref-get-doi-at-point)))
+
- ;; quit
- ((or
- (= choice ?q) ; q
- (= choice ?\ )) ; space
- ;; this clears the minibuffer
- (message ""))
+(defun org-ref-wos-related-at-point ()
+ "open the doi in wos related articles for bibtex key under point."
+ (interactive)
+ (doi-utils-wos-related (org-ref-get-doi-at-point)))
- ;; pdf
- ((= choice ?p)
- (org-ref-open-pdf-at-point))
- ;; notes
- ((= choice ?n)
- (org-ref-open-notes-at-point))
+(defun org-ref-google-scholar-at-point ()
+ "open the doi in google scholar for bibtex key under point."
+ (interactive)
+ (doi-utils-google-scholar (org-ref-get-doi-at-point)))
+
- ;; url
- ((= choice ?u)
- (org-ref-open-url-at-point))
+(defun org-ref-pubmed-at-point ()
+ "open the doi in pubmed for bibtex key under point."
+ (interactive)
+ (doi-utils-pubmed (org-ref-get-doi-at-point)))
+
+
+(defun org-ref-crossref-at-point ()
+ "open the doi in crossref for bibtex key under point."
+ (interactive)
+ (doi-utils-crossref (org-ref-get-doi-at-point)))
- ;; anything else we just quit.
- (t (message "")))))
-
+
+(defun org-ref-cite-onclick-minibuffer-menu (&optional link-string)
+ "action when a cite link is clicked on.
+Provides a menu of context sensitive actions. If the bibtex entry has a pdf, you get an option to open it. If there is a doi, you get a lot of options."
+ (interactive)
+ (let* ((results (org-ref-get-bibtex-key-and-file))
+ (key (car results))
+ (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
+ (bibfile (cdr results))
+ (url (save-excursion
+ (with-temp-buffer
+ (insert-file-contents bibfile)
+ (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
+ (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
+ 'org-ref-cite-menu-funcs
+ '("o" "pen" org-ref-open-citation-at-point)))
+
+ ;; pdf
+ (when (file-exists-p pdf-file)
+ (add-to-list
+ 'org-ref-cite-menu-funcs
+ `("p" "df" ,org-ref-open-pdf-function) t))
+
+ ;; notes
+ (add-to-list
+ 'org-ref-cite-menu-funcs
+ '("n" "otes" org-ref-open-notes-at-point) t)
+
+ ;; url
+ (when (or url doi)
+ (add-to-list
+ 'org-ref-cite-menu-funcs
+ '("u" "rl" org-ref-open-url-at-point) t))
+
+ ;; doi funcs
+ (when doi
+ (add-to-list
+ 'org-ref-cite-menu-funcs
+ '("w" "os" org-ref-wos-at-point) t)
+
+ (add-to-list
+ 'org-ref-cite-menu-funcs
+ '("c" "iting" org-ref-wos-citing-at-point) t)
+
+ (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)
+
+ (add-to-list
+ 'org-ref-cite-menu-funcs
+ '("P" "ubmed" org-ref-pubmed-at-point) t))
+
+ ;; add user functions
+ (dolist (tup org-ref-user-cite-menu-funcs)
+ (add-to-list
+ 'org-ref-cite-menu-funcs
+ tup t))
+
+ ;; finally quit
+ (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 "")))
+ ;; get the input
+ (let* ((input (read-char-exclusive))
+ (choice (assoc
+ (char-to-string input) org-ref-cite-menu-funcs)))
+ ;; now run the function (2nd element in choice)
+ (when choice
+ (funcall
+ (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.
@@ -1426,23 +1681,23 @@ 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
@@ -1458,10 +1713,10 @@ 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 "%s" key key))
(org-ref-split-and-strip-string keyword) ","))
@@ -1478,7 +1733,7 @@ We will want to generate formatting functions for each citation type. The reason
-We create the links by mapping the function onto the list of defined link types.
+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)
@@ -1491,22 +1746,22 @@ 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)
@@ -1514,7 +1769,7 @@ 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
@@ -1534,39 +1789,41 @@ 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
@@ -1577,10 +1834,10 @@ 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
@@ -1601,8 +1858,8 @@ 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))))))
@@ -1611,13 +1868,169 @@ org-mode already defines a store link function for bibtex entries. It does not s
(car org-stored-links)))
#+END_SRC
+** Index entries
+org-ref minimally supports index entries. To make an index in a file, you should put in the LaTeX header these lines
+
+
+#+LATEX_HEADER: \usepackage{makeidx}
+#+LATEX_HEADER: \makeindex
+
+
+Finally, put \makeindex at the end of the document where you want the index to appear. You will need to run the makeindex program at an appropriate point in your LaTeX to pdf, or use ox-manuscript, which will do it for you.
+
+
+Use index links to create entries (see http://en.wikibooks.org/wiki/LaTeX/Indexing). Clicking on an index link runs occur on the buffer for the entry. The link exports to LaTeX. Some links may need to be enclosed in double brackets if they have spaces in them.
+
+
+index:hello
+index:hello!Peter
+[[index:hello!Sam@\textsl{Sam}]]
+[[index:Lin@\textbf{Lin}]]
+[[index:Joe|textit]]
+[[index:Lin@\textbf{Lin}]]
+[[index:Peter|see {hello}]]
+[[index:Jen|seealso{Jenny}]]
+
+index:encodings!input!cp850
+
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(org-add-link-type
+ "index"
+ (lambda (path)
+ (occur path))
+
+ (lambda (path desc format)
+ (cond
+ ((eq format 'latex)
+ (format "\\index{%s}" path)))))
+
+;; this will generate a temporary index of entries in the file.
+(org-add-link-type
+ "printindex"
+ (lambda (path)
+ (let ((*index-links* '())
+ (*initial-letters* '()))
+
+ ;; get links
+ (org-element-map (org-element-parse-buffer) 'link
+ (lambda (link)
+ (let ((type (nth 0 link))
+ (plist (nth 1 link)))
+
+ (when (equal (plist-get plist ':type) "index")
+ (add-to-list
+ '*index-links*
+ (cons (plist-get plist :path)
+ (format
+ "[[elisp:(progn (switch-to-buffer \"%s\") (goto-char %s))][%s]]"
+(current-buffer)
+ (plist-get plist :begin) ;; position of link
+ ;; grab a description
+ (save-excursion
+ (goto-char (plist-get plist :begin))
+ (if (thing-at-point 'sentence)
+ ;; get a sentence
+ (replace-regexp-in-string
+ "\n" "" (thing-at-point 'sentence))
+ ;; or call it a link
+ "link")))))))))
+
+ ;; 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))
+
+ ;; now create the index
+ (switch-to-buffer (get-buffer-create "*index*"))
+ (org-mode)
+ (erase-buffer)
+ (insert "#+TITLE: Index\n\n")
+ (dolist (letter *initial-letters*)
+ (insert (format "* %s\n" (upcase letter)))
+ ;; now process the links
+ (while (and
+ ,*index-links*
+ (string= letter (substring (car (car *index-links*)) 0 1)))
+ (let ((link (pop *index-links*)))
+ (insert (format "%s %s\n\n" (car link) (cdr link))))))
+ (switch-to-buffer "*index*")))
+ ;; formatting
+ (lambda (path desc format)
+ (cond
+ ((eq format 'latex)
+ (format "\\printindex")))))
+#+END_SRC
+
+#+RESULTS:
+| lambda | (path) | (let ((*index-links* (quote nil)) (*initial-letters* (quote nil))) (org-element-map (org-element-parse-buffer) (quote link) (lambda (link) (let ((type (nth 0 link)) (plist (nth 1 link))) (when (equal (plist-get plist (quote :type)) index) (add-to-list (quote *index-links*) (cons (plist-get plist :path) (format [[elisp:(progn (switch-to-buffer "%s") (goto-char %s))][%s]] (current-buffer) (plist-get plist :begin) (save-excursion (goto-char (plist-get plist :begin)) (if (thing-at-point (quote sentence)) (replace-regexp-in-string \n (thing-at-point (quote sentence))) link))))))))) (setq *index-links* (cl-sort *index-links* (quote string-lessp) :key (quote car))) (dolist (link *index-links*) (add-to-list (quote *initial-letters*) (substring (car link) 0 1) t)) (switch-to-buffer (get-buffer-create *index*)) (org-mode) (erase-buffer) (insert #+TITLE: Index\n\n) (dolist (letter *initial-letters*) (insert (format * %s\n (upcase letter))) (while (and *index-links* (string= letter (substring (car (car *index-links*)) 0 1))) (let ((link (pop *index-links*))) (insert (format %s %s\n\n (car link) (cdr link)))))) (switch-to-buffer *index*)) |
+| lambda | (path desc format) | (cond ((eq format (quote latex)) (format \printindex))) |
+
+** 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
+
+And at the end of the document put \makeglossaries.
+
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(org-add-link-type
+ "newglossaryentry"
+ nil ;; no follow action
+ (lambda (path desc format)
+ (cond
+ ((eq format 'latex)
+ (format "\\newglossaryentry{%s}{%s}" path desc)))))
+
+
+;; link to entry
+(org-add-link-type
+ "gls"
+ nil ;; no follow action
+ (lambda (path desc format)
+ (cond
+ ((eq format 'latex)
+ (format "\\gls{%s}" path)))))
+
+;; plural
+(org-add-link-type
+ "glspl"
+ nil ;; no follow action
+ (lambda (path desc format)
+ (cond
+ ((eq format 'latex)
+ (format "\\glspl{%s}" path)))))
+
+;; capitalized link
+(org-add-link-type
+ "Gls"
+ nil ;; no follow action
+ (lambda (path desc format)
+ (cond
+ ((eq format 'latex)
+ (format "\\Gls{%s}" path)))))
+
+;; capitalized link
+(org-add-link-type
+ "Glspl"
+ nil ;; no follow action
+ (lambda (path desc format)
+ (cond
+ ((eq format 'latex)
+ (format "\\Glspl{%s}" path)))))
+#+END_SRC
+
+
* 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))
@@ -1724,20 +2137,17 @@ 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 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)
- (progn
- (org-show-entry)
- (outline-previous-visible-heading 1)
- (recenter-top-bottom 0))
- ;; no entry found, so add one
+ (funcall org-ref-open-notes-function)
+ ;; no entry found, so add one
(insert (format "\n** TODO %s - %s" year title))
(insert (format"
:PROPERTIES:
@@ -1755,6 +2165,25 @@ key author journal year volume pages doi url key org-ref-pdf-directory key))
(save-buffer))))
#+END_SRC
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(defun org-ref-open-notes-from-reftex ()
+ "Call reftex, and open notes for selected entry."
+ (interactive)
+ (let ((bibtex-key )))
+
+ ;; 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))
+
+ (re-search-forward (format
+ ":Custom_ID: %s$"
+ (first (reftex-citation t)) nil 'end))
+ (funcall org-ref-open-notes-function))
+#+END_SRC
+
** open url in browser from bibtex
We bind this to a key here [[*key%20bindings%20for%20utilities][key bindings for utilities]].
@@ -1805,7 +2234,7 @@ Relies on the python script /upload_bibtex_citeulike.py being in the user direct
#+END_SRC
*** The upload script
-Here is the python script for uploading.
+Here is the python script for uploading.
*************** TODO document how to get the cookies
*************** END
@@ -1868,7 +2297,7 @@ print r
(shell-command (concat "pdflatex " bib-base))
(kill-buffer texfile)
(org-open-file pdffile)
- ))
+ ))
#+END_SRC
** Extract bibtex entries cited in an org-file
@@ -1885,20 +2314,20 @@ If no bibliography is in the buffer the `reftex-default-bibliography' is used."
(contents (buffer-string))
(cb (current-buffer))
basename texfile bibfile results)
-
+
;; open tempfile and insert org-buffer contents
(find-file tempname)
(insert contents)
- (setq basename (file-name-sans-extension
+ (setq basename (file-name-sans-extension
(file-name-nondirectory buffer-file-name))
texfile (concat tempname ".tex")
bibfile (concat tempname ".bib"))
-
+
;; see if we have a bibliography, and insert the default one if not.
(save-excursion
(goto-char (point-min))
(unless (re-search-forward "^bibliography:" (point-max) 'end)
- (insert (format "\nbibliography:%s"
+ (insert (format "\nbibliography:%s"
(mapconcat 'identity reftex-default-bibliography ",")))))
(save-buffer)
@@ -1946,7 +2375,7 @@ Depending on how you enter citations, you may have citations with no correspondi
(found nil))
(dolist (arg list i)
(if (string-match (concat "^" substring "$") arg)
- (progn
+ (progn
(setq found t)
(return i)))
(setq i (+ i 1)))
@@ -1966,8 +2395,8 @@ Makes a new buffer with clickable links."
(bad-citations '()))
(org-element-map (org-element-parse-buffer) 'link
- (lambda (link)
- (let ((plist (nth 1 link)))
+ (lambda (link)
+ (let ((plist (nth 1 link)))
(when (equal (plist-get plist ':type) "cite")
(dolist (key (org-ref-split-and-strip-string (plist-get plist ':path)) )
(when (not (index key bibtex-keys))
@@ -1993,7 +2422,7 @@ Makes a new buffer with clickable links."
#+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 ()
@@ -2028,16 +2457,16 @@ 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)
@@ -2053,7 +2482,7 @@ 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))
@@ -2080,7 +2509,7 @@ 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)
@@ -2090,7 +2519,7 @@ 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.
@@ -2129,7 +2558,7 @@ 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.
@@ -2139,7 +2568,7 @@ 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
@@ -2168,14 +2597,14 @@ 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
@@ -2197,7 +2626,7 @@ 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))
@@ -2210,18 +2639,115 @@ 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))
+ (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 add it to a hook that updates after every command, including cursor movements.
+
+ref:test citep:test label:rett
+
+#+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))))))))
+
+
+(defun org-ref-link-message ()
+ "Print a minibuffer message about the link that point is on."
+ (interactive)
+ (let* ((object (org-element-context))
+ (type (org-element-property :type object)))
+ (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 (org-ref-get-label-context
+ (org-element-property :path object))))
+
+ ((string= type "eqref")
+ (message (org-ref-get-label-context
+ (org-element-property :path object))))
+
+ ;; message the count
+ ((string= type "label")
+ (let ((count (org-ref-count-labels
+ (org-element-property :path object))))
+ ;; get plurality on occurrence correct
+ (message (concat
+ (number-to-string count)
+ " occurence"
+ (when (or (= count 0)
+ (> count 1))
+ "s")))))))))
+
+
+(when org-ref-show-citation-on-enter
+ (add-hook 'post-command-hook 'org-ref-link-message))
+#+END_SRC
+
* Aliases
I like convenience. Here are some aliases for faster typing.
@@ -2231,6 +2757,7 @@ I like convenience. Here are some aliases for faster typing.
(defalias 'orp 'org-ref-open-pdf-at-point)
(defalias 'oru 'org-ref-open-url-at-point)
(defalias 'orn 'org-ref-open-notes-at-point)
+(defalias 'ornr 'org-ref-open-notes-from-reftex)
(defalias 'orib 'org-ref-insert-bibliography-link)
(defalias 'oric 'org-ref-insert-cite-link)
@@ -2239,17 +2766,239 @@ I like convenience. Here are some aliases for faster typing.
(defalias 'orcb 'org-ref-clean-bibtex-entry)
#+END_SRC
+* Helm interface
+[[https://github.com/tmalsburg/helm-bibtex][helm-bibtex]] is a very cool interface to bibtex files. Out of the box though, it is not super convenient for org-ref. Here, we modify it to make it fit our workflow and extend it where needed.
+
+1. Make the default action to insert selected keys.
+2. Make open entry second action
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(setq helm-source-bibtex
+ '((name . "BibTeX entries")
+ (init . helm-bibtex-init)
+ (candidates . helm-bibtex-candidates)
+ (filtered-candidate-transformer . helm-bibtex-candidates-formatter)
+ (action . (("Insert citation" . helm-bibtex-insert-citation)
+ ("Show entry" . helm-bibtex-show-entry)
+ ("Open PDF file (if present)" . helm-bibtex-open-pdf)
+ ("Open URL or DOI in browser" . helm-bibtex-open-url-or-doi)
+ ("Insert reference" . helm-bibtex-insert-reference)
+ ("Insert BibTeX key" . helm-bibtex-insert-key)
+ ("Insert BibTeX entry" . helm-bibtex-insert-bibtex)
+ ("Attach PDF to email" . helm-bibtex-add-PDF-attachment)
+ ("Edit notes" . helm-bibtex-edit-notes)
+ ))))
+#+END_SRC
+
+Now, let us define a function that inserts the cite links:
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(defun helm-bibtex-format-org-ref (keys)
+ "Insert selected KEYS as cite link. Append KEYS if you are on a link.
+Technically, this function should return a string that is inserted by helm. This function does the insertion and gives helm an empty string to insert. This lets us handle appending to a link properly."
+ (let* ((object (org-element-context)))
+ (cond
+ ;; case where we are in a link
+ ((and (equal (org-element-type object) 'link)
+ (-contains?
+ org-ref-cite-types
+ (org-element-property :type object)))
+ (goto-char (org-element-property :end object))
+ ;; sometimes there are spaces at the end of the link
+ ;; this code moves point pack until no spaces are there
+ (while (looking-back " ") (backward-char))
+ (insert (concat "," (mapconcat 'identity keys ","))))
+
+ ;; We are next to a link, and we want to append
+ ((save-excursion
+ (backward-char)
+ (and (equal (org-element-type (org-element-context)) 'link)
+ (-contains?
+ org-ref-cite-types
+ (org-element-property :type (org-element-context)))))
+ (goto-char (org-element-property :end object))
+ (while (looking-back " ") (backward-char))
+ (insert (concat "," (mapconcat 'identity keys ","))))
+
+ ;; insert fresh link
+ (t
+ (insert
+ (concat (if helm-current-prefix-arg
+ (ido-completing-read "Type: " org-ref-cite-types)
+ org-ref-default-citation-link)
+ ":"
+ (s-join "," keys))))))
+ ;; return empty string for helm
+ "")
+
+(setq helm-bibtex-format-citation-functions
+ '((org-mode . helm-bibtex-format-org-ref)))
+
+(defun org-ref-helm-insert-cite-link ()
+ "org-ref function to use helm on the bibliography defined in the org-file."
+ (interactive)
+ (let ((helm-bibtex-bibliography (org-ref-find-bibliography)))
+ (helm-bibtex)))
+
+(require 'helm-bibtex)
+#+END_SRC
+
+** A helm click menu
+This code provides a helm interface to things you can do when you click on a citation link. This is an alternative to the minibuffer menu.
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(defun org-ref-get-citation-string-at-point ()
+ "Get a string of a formatted citation"
+ (interactive)
+ (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)))))
+
+(defun org-ref-cite-candidates ()
+ "Generate the list of possible candidates for click actions on a cite link.
+Checks for pdf and doi, and add appropriate functions."
+ (interactive)
+ (let* ((results (org-ref-get-bibtex-key-and-file))
+ (key (car results))
+ (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
+ (bibfile (cdr results))
+ (url (save-excursion
+ (with-temp-buffer
+ (insert-file-contents bibfile)
+ (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
+ (bibtex-autokey-get-field "doi"))))
+ (candidates `(("Quit" . org-ref-citation-at-point)
+ ("Open bibtex entry" . org-ref-open-citation-at-point))))
+ ;; for some reason, when there is no doi or url, they are returned as "". I
+ ;; prefer nil so we correct this here.
+ (when (string= doi "") (setq doi nil))
+ (when (string= url "") (setq url nil))
+
+ ;; Conditional pdf functions
+ (if (file-exists-p pdf-file)
+ (add-to-list
+ 'candidates
+ '("Open pdf" . org-ref-open-pdf-at-point)
+ t)
+ (add-to-list
+ 'candidates
+ '("Try to get pdf" . (lambda ()
+ (save-window-excursion
+ (org-ref-open-citation-at-point)
+ (bibtex-beginning-of-entry)
+ (doi-utils-get-bibtex-entry-pdf))))
+ t))
+
+
+ (add-to-list
+ 'candidates
+ '("Open notes" . org-ref-open-notes-at-point)
+ t)
+
+ ;; conditional url and doi functions
+ (when (or url doi)
+ (add-to-list
+ 'candidates
+ '("Open in browser" . org-ref-open-url-at-point)
+ t))
+
+ (when doi
+ (mapc (lambda (x)
+ (add-to-list 'candidates x t))
+ `(("WOS" . org-ref-wos-at-point)
+ ("Related articles in WOS" . org-ref-wos-related-at-point)
+ ("Citing articles in WOS" . org-ref-wos-citing-at-point)
+ ("Google Scholar" . org-ref-google-scholar-at-point)
+ ("Pubmed" . org-ref-pubmed-at-point)
+ ("Crossref" . org-ref-crossref-at-point)
+ )))
+
+ (add-to-list
+ 'candidates
+ '("Copy formatted citation to clipboard" . org-ref-copy-entry-as-summary)
+ t)
+
+ (add-to-list
+ 'candidates
+ '("Copy key to clipboard" . (lambda ()
+ (kill-new
+ (car (org-ref-get-bibtex-key-and-file)))))
+ t)
+
+ (add-to-list
+ 'candidates
+ '("Copy bibtex entry to file" . org-ref-copy-entry-at-point-to-file)
+ t)
+
+ (add-to-list
+ 'candidates
+ '("Email bibtex entry and pdf" . (lambda ()
+ (save-excursion
+ (org-ref-open-citation-at-point)
+ (email-bibtex-entry))))
+ t)
+ ;; finally return a numbered list of the candidates
+ (loop for i from 0
+ for cell in candidates
+ collect (cons (format "%2s. %s" i (car cell))
+ (cdr cell)))))
+
+
+(defvar org-ref-helm-user-candidates '()
+ "List of user-defined candidates to act when clicking on a cite link.
+This is a list of cons cells '((\"description\" . action)). The action function should not take an argument, and should assume point is on the cite key of interest.
+")
+
+;; example of adding your own function
+(add-to-list
+ 'org-ref-helm-user-candidates
+ '("Example" . (lambda () (message-box "You did it!")))
+ t)
+
+(defun org-ref-cite-click-helm (key)
+ "subtle points.
+1. get name and candidates before entering helm because we need the org-buffer.
+2. switch back to the org buffer before evaluating the action. most of them need the point and buffer."
+ (interactive)
+ (let ((name (org-ref-get-citation-string-at-point))
+ (candidates (org-ref-cite-candidates))
+ (cb (current-buffer)))
+
+ (helm :sources `(((name . ,name)
+ (candidates . ,candidates)
+ (action . (lambda (f)
+ (switch-to-buffer cb)
+ (funcall f))))
+ ((name . "User functions")
+ (candidates . ,org-ref-helm-user-candidates)
+ (action . (lambda (f)
+ (switch-to-buffer cb)
+ (funcall f))))
+ ))))
+#+END_SRC
+
+#+RESULTS:
+: org-ref-cite-click-helm
+
* End of code
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(provide 'org-ref)
#+END_SRC
-
* Build :noexport:
+This code will tangle the elisp code out to org-ref.el and load it.
[[elisp:(progn (org-babel-tangle) (load-file "org-ref.el"))]]
-[[elisp:(org-babel-load-file "org-ref.org")]]
-
-
+Alternatively you may use:
+[[elisp:(org-babel-load-file "org-ref.org")]]