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
;;; 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
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(require 'reftex-cite)
(require 'dash)
+(require 'helm)
+(require 'helm-bibtex)
#+END_SRC
** Custom variables
"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.
"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)
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))
+ (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)
+
+(when org-ref-show-citation-on-enter
+ (setq org-ref-message-timer
+ (run-with-idle-timer 0.5 t 'org-ref-link-message)))
+
+(defun org-ref-show-link-messages ()
+ "Turn on link messages. You will see a message in the
+minibuffer when on a cite, ref or label link."
+ (interactive)
+ (setq org-ref-message-timer
+ (run-with-idle-timer 0.5 t 'org-ref-link-message))
+ )
+(defun org-ref-cancel-link-messages ()
+ "Stop showing messages in minibuffer when on a link."
+ (interactive)
+ (cancel-timer org-ref-message-timer))
+
+;; this approach caused the selected region to not be highlighted any more.
+; (add-hook 'post-command-hook 'org-ref-link-message))
+; (remove-hook 'post-command-hook 'org-ref-link-message))
(add-hook 'org-mode-hook 'org-mode-reftex-setup)
)))))
#+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
(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)
(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))))))
(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
"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)))))))))
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)))
I do not have plans to make a numbered bibliography with numbered citations anytime soon. This will require changing the way the citation links are exported, and keeping track of the numbers.
+*** An org bibliography
+You can export an org-file to an org-file or org-buffer (org-org-epxort-as-org). In this case, it would be useful convert the cite links to links to custom_ids, and the bibliography link to a first-level heading Bibliography with org-bibtex like headings for each entry. This code should enable this. Right now, it does not appear to work for org export though.
+
+First, we get the string for a single entry.
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(defun org-ref-get-bibtex-entry-org (key)
+ "returns an org string for the bibliography entry corresponding to key"
+ (let ((org-ref-bibliography-files (org-ref-find-bibliography))
+ (file) (entry) (bibtex-entry) (entry-type) (format))
+
+ (setq file (catch 'result
+ (loop for file in org-ref-bibliography-files do
+ (if (org-ref-key-in-file-p key (file-truename file))
+ (throw 'result file)
+ (message "%s not found in %s" key (file-truename file))))))
+
+ (with-temp-buffer
+ (insert-file-contents file)
+ (bibtex-search-entry key nil 0)
+ (setq entry (bibtex-parse-entry))
+ (format "** %s - %s
+ :PROPERTIES:
+ %s
+ :END:
+" (org-ref-reftex-get-bib-field "author" entry)
+(org-ref-reftex-get-bib-field "title" entry)
+(concat " :CUSTOM_ID: " (org-ref-reftex-get-bib-field "=key=" entry) "\n"
+ (mapconcat (lambda (element) (format " :%s: %s"
+ (upcase (car element))
+ (cdr element)))
+ entry
+ "\n"))))))
+#+END_SRC
+
+Now, we loop over the keys, and combine all the entries into a bibliography.
+#+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)))
+ (when keys
+ (concat "* Bibliography
+"
+ (mapconcat (lambda (x) (org-ref-get-bibtex-entry-org x)) keys "\n")
+ "\n"))))
+#+END_SRC
+
+*** An ascii bibliography
+
+This function gets the html for one entry.
+
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(defun org-ref-get-bibtex-entry-ascii (key)
+ "returns an ascii string for the bibliography entry corresponding to key"
+
+ (format "[%s] %s" key (org-ref-get-bibtex-entry-citation key)))
+#+END_SRC
+
+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
+(defun org-ref-get-ascii-bibliography ()
+ "Create an html bibliography when there are keys"
+ (let ((keys (org-ref-get-bibtex-keys)))
+ (when keys
+ (concat
+"Bibliography
+=============
+"
+ (mapconcat (lambda (x) (org-ref-get-bibtex-entry-ascii x)) keys "\n")
+ "\n"))))
+#+END_SRC
+
+
*** the links
We use a link for the bibliography so that we can click on it to open the bibliography file. The link may have more than one bibliography file in it, separated by commas. Clicking opens the file under the cursor. The bibliographies should be full filenames with the bib extension. Clicking on this link makes reftex-default-bibliography local and sets it to the list of files in the link. We need this to use reftex's searching capability.
;; 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
;; 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
;; 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" "" keyword))))))
+ ;; 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-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 "{\\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
(lambda (arg) (message "Nothing implemented for clicking here."))
(lambda (keyword desc format)
(cond
+ ((eq format 'org) (org-ref-get-org-bibliography))
((eq format 'html) (org-ref-get-html-bibliography))
((eq format 'latex)
- ;; write out the latex bibliography command
- (format "\\printbibliography" keyword)))))
+ ;; write out the biblatex bibliography command
+ "\\printbibliography"))
+))
#+END_SRC
We also create a bibliographystyle link. There is nothing to do on clicking here, and we create it for consistency. This sets the style for latex export, so use something appropriate there, e.g. unsrt, plain, plainnat, ...
#+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)
;; 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
;; 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
(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)
(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)
(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)
(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)
#+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) 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 ((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)))))
+ (message (format "%s occurences" (org-ref-count-labels label))))
(lambda (keyword desc format)
(cond
((eq format 'html) (format "(<label>%s</label>)" path))
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-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"
#+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.
(unless
(or
;; our label links
- (progn
+ (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-*\\(%s\\)\\b" label) nil t))
-
+
;; org tblname
(progn
(goto-char (point-min))
;; 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)
(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)))))))
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)
#+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
(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
+
+Let us make a helm function to insert a label link. This will help you enter unique labels.
+#+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
+ (action . (lambda (label)
+ (switch-to-buffer ,cb)
+ (insert
+ (concat
+ "label:"
+ (or label
+ helm-pattern))))))))))
#+END_SRC
Now we create the completion function. This works from the org-machinery, e.g. if you type C-c C-l to insert a link, and use completion by pressing tab.
(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.
+"
+ (interactive)
+ (let* ((labels (org-ref-get-labels))
+ (contexts (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)))
+ ))))))))
+#+END_SRC
+
+#+RESULTS:
+: org-ref-helm-insert-ref-link
+
** pageref
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))
(progn
(goto-char (point-min))
(re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
-
+
;; org tblname
(progn
(goto-char (point-min))
** 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"
(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.
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.
+ (let ((cp (point)))
+ (goto-char (org-element-property :begin object))
+ (search-forward link-string (org-element-property :end object))
+ (goto-char (match-beginning 0))
+ ;; 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))
(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))
(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)))
#+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: ")
-
- (with-temp-buffer
- (insert-file-contents filename)
- (prog1
- (bibtex-search-entry key nil 0))))
+ (save-current-buffer
+ (let ((bibtex-files (list filename)))
+ (bibtex-search-entry key t))))
#+END_SRC
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
(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)
(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)
#+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
+(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.")
-#+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.
-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)))))
- (cond
- ;; open
- ((= choice ?o)
- (find-file bibfile)
- (bibtex-search-entry key))
- ;; cite
- ((= choice ?c)
- (org-ref-citation-at-point))
-
+;; 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)))
+
+
+(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 ""))
- ;; pdf
- ((= choice ?p)
- (org-ref-open-pdf-at-point))
+(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)))
- ;; notes
- ((= choice ?n)
- (org-ref-open-notes-at-point))
- ;; url
- ((= choice ?u)
- (org-ref-open-url-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)))
- ;; anything else we just quit.
- (t (message "")))))
-
+
+(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)))
+
+
+(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.
#+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
- ((eq format 'html)
- (mapconcat
- (lambda (key)
+ ((eq format 'org)
+ (mapconcat
+ (lambda (key)
+ (format "[[#%s][%s]]" key key))
+ (org-ref-split-and-strip-string keyword) ","))
+
+ ((eq format 'ascii)
+ (concat "["
+ (mapconcat
+ (lambda (key)
+ (format "%s" key))
+ (org-ref-split-and-strip-string keyword) ",") "]"))
+
+ ((eq format 'html)
+ (mapconcat
+ (lambda (key)
(format "<a href=\"#%s\">%s</a>" key key))
(org-ref-split-and-strip-string keyword) ","))
-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)
(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)
;; 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
(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
#+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
(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))))))
(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))
(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.
- (unless (re-search-forward (format ":Custom_ID: %s$" key) nil 'end)
+ (if (re-search-forward (format ":Custom_ID: %s$" key) nil 'end)
+ (funcall org-ref-open-notes-function)
+ ;; no entry found, so add one
(insert (format "\n** TODO %s - %s" year title))
(insert (format"
:PROPERTIES:
(save-buffer))))
#+END_SRC
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(defun org-ref-open-notes-from-reftex ()
+ "Call reftex, and open notes for selected entry."
+ (interactive)
+ (let ((bibtex-key )))
+
+ ;; now look for entry in the notes file
+ (if org-ref-bibliography-notes
+ (find-file-other-window org-ref-bibliography-notes)
+ (error "org-ref-bib-bibliography-notes is not set to anything"))
+
+ (goto-char (point-min))
+
+ (re-search-forward (format
+ ":Custom_ID: %s$"
+ (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]].
#+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
(shell-command (concat "pdflatex " bib-base))
(kill-buffer texfile)
(org-open-file pdffile)
- ))
+ ))
#+END_SRC
** Extract bibtex entries cited in an org-file
(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)
#+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
(found nil))
(dolist (arg list i)
(if (string-match (concat "^" substring "$") arg)
- (progn
+ (progn
(setq found t)
(return i)))
(setq i (+ i 1)))
(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))
(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)))
+ ))))
+ (goto-char cp)
+ bad-citations))
+
+;; It seems I forgot I already defined this earlier!
+;; (defun org-ref-get-labels ()
+;; "Returns a list of known labels in the org document. These include label links, latex labels, label tags, and table names. The list contains all labels, not just unique ones.
+;; "
+;; (let ((cp (point))
+;; (labels '()))
+;; (goto-char (point-min))
+;; (while (re-search-forward "[^#+]label:\\(.*\\)\\s-" nil t)
+;; (push (match-string 1) labels))
+
+;; (goto-char (point-min))
+;; (while (re-search-forward "\\label{\\(.*\\)}\\s-?" nil t)
+;; (push (match-string 1) labels))
+
+;; (goto-char (point-min))
+;; (while (re-search-forward "^#\\+label:\\s-*\\(.*\\)" nil t)
+;; (push (match-string 1) labels))
+
+;; (goto-char (point-min))
+;; (while (re-search-forward "^#\\+tblname:\\s-*\\(.*\\)" nil t)
+;; (push (match-string 1) labels))
+;; ;; check for CUSTOM_ID
+;; (org-map-entries
+;; (lambda ()
+;; (when (org-entry-get (point) "CUSTOM_ID")
+;; (push (org-entry-get (point) "CUSTOM_ID") labels))))
+;; ;; return to original place
+;; (goto-char cp)
+;; labels))
+
+
+(defun org-ref-bad-ref-candidates ()
+ "Returns a list of conses (ref . marker) where ref is a ref link that does not point to anything (i.e. a label)."
+ ;; 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 ()
(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)
(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))
;; 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)
;; 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.
(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.
(save-excursion
(funcall x))))
org-ref-clean-bibtex-entry-hook)
-
+
;; sort fields within entry
(org-ref-sort-bibtex-entry)
;; check for non-ascii characters
(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
(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))
(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 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)))))
+
+ ;; maybe we have a CUSTOM-ID
+ (org-map-entries
+ (lambda () (when (string=
+ label
+ (org-entry-get (point) "CUSTOM_ID"))
+ (throw 'result (org-get-heading)))))
+ (beep)
+ (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 (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
+ (when (> count 1) (beep))
+ (message (concat
+ (number-to-string count)
+ " occurence"
+ (when (or (= count 0)
+ (> count 1))
+ "s")))))
+
+ ;; check if the bibliography files exist.
+ ((string= type "bibliography")
+ (let* ((bibfile)
+ ;; object is the link you clicked on
+ (object (org-element-context))
+ (link-string (org-element-property :path object))
+ (link-string-beginning)
+ (link-string-end))
+
+ (save-excursion
+ (goto-char (org-element-property :begin object))
+ (search-forward link-string nil nil 1)
+ (setq link-string-beginning (match-beginning 0))
+ (setq link-string-end (match-end 0)))
+
+ ;; 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
+ (goto-char link-string-beginning)
+ (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
+ (goto-char link-string-beginning)
+ (if (search-backward "," link-string-beginning 1 1)
+ (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
+ (setq key-beginning (point)))) ; no match found
+ ;; save the key we clicked on.
+ (setq bibfile
+ (org-ref-strip-string
+ (buffer-substring key-beginning key-end)))
+ (if (file-exists-p bibfile)
+ (message "%s exists." bibfile)
+ (beep)
+ (message "!!! %s NOT FOUND !!!" bibfile))))
+ )))))
+#+END_SRC
+
* Aliases
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)
(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.
+
+In the helm-bibtex buffer, C-u will give you a helm menu to select a new link type for the selected entries.
+
+C-u C-u will change the key at point to the selected keys.
+"
+ (let* ((object (org-element-context))
+ (last-char (save-excursion
+ (goto-char (org-element-property :end object))
+ (backward-char)
+ (if (looking-at " ")
+ " "
+ ""))))
+ (cond
+ ;; case where we are in a link
+ ((and (equal (org-element-type object) 'link)
+ (-contains?
+ org-ref-cite-types
+ (org-element-property :type object)))
+ (cond
+ ;; no prefix. append keys
+ ((equal helm-current-prefix-arg nil)
+ (goto-char (org-element-property :end object))
+ (while (looking-back " ") (backward-char))
+ (insert (concat "," (mapconcat 'identity keys ","))))
+ ;; double prefix, replace key at point
+ ((equal helm-current-prefix-arg '(16))
+ (setf (buffer-substring
+ (org-element-property :begin object)
+ (org-element-property :end object))
+ (concat
+ (replace-regexp-in-string
+ (car (org-ref-get-bibtex-key-and-file)) ; key
+ (mapconcat 'identity keys ",") ; new keys
+ (org-element-property :raw-link object)
+ )
+ ;; replace space at end to avoid collapsing into next word.
+ last-char)))
+ (t
+ (message "Not found"))))
+
+ ;; We are next to a link, and we want to append
+ ;; next to a link means one character back is on a link.
+ ((save-excursion
+ (backward-char)
+ (and (equal (org-element-type (org-element-context)) 'link)
+ (-contains?
+ org-ref-cite-types
+ (org-element-property :type (org-element-context)))))
+ (while (looking-back " ") (backward-char))
+ (insert (concat "," (mapconcat 'identity keys ","))))
+
+ ;; insert fresh link
+ (t
+ ;;(message-box "fresh link")
+ (insert
+ (concat (if (equal helm-current-prefix-arg '(4))
+ (helm :sources `((name . "link types")
+ (candidates . ,org-ref-cite-types)
+ (action . (lambda (x) x))))
+ org-ref-default-citation-link)
+ ":"
+ (s-join "," keys))))))
+ ;; return empty string for helm
+ "")
+
+(setq helm-bibtex-format-citation-functions
+ '((org-mode . helm-bibtex-format-org-ref)))
+
+(defun org-ref-helm-insert-cite-link (arg)
+ "org-ref function to use helm-bibtex to insert a citation link.
+With one prefix arg, insert a ref link.
+With two prefix args, insert a label link."
+ (interactive "P")
+ (cond
+ ((equal arg nil)
+ (let ((helm-bibtex-bibliography (org-ref-find-bibliography)))
+ (helm-bibtex)))
+ ((equal arg '(4))
+ (org-ref-helm-insert-ref-link))
+ ((equal arg '(16))
+ (org-ref-helm-insert-label-link))))
+
+(require 'helm-bibtex)
+
+;; add our own fallback entries where we want them. These appear in reverse order of adding in the menu
+(setq helm-bibtex-fallback-options
+ (-insert-at 1 '("Crossref" . "http://search.crossref.org/?q=%s") helm-bibtex-fallback-options))
+
+(setq helm-bibtex-fallback-options
+ (-insert-at
+ 1
+ '("Scopus" . "http://www.scopus.com/scopus/search/submit/xadvanced.url?searchfield=TITLE-ABS-KEY(%s)")
+ helm-bibtex-fallback-options))
+
+(setq helm-bibtex-fallback-options
+ (-insert-at 1 '("Open Web of Science" . (lambda () (browse-url "http://apps.webofknowledge.com")))
+ helm-bibtex-fallback-options))
+#+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)))
+ (if bibfile
+ (save-excursion
+ (with-temp-buffer
+ (insert-file-contents bibfile)
+ (bibtex-search-entry key)
+ (org-ref-bib-citation)))
+ (beep)
+ "!!! No entry found !!!" )))
+
+(defun org-ref-cite-candidates ()
+ "Generate the list of possible candidates for click actions on a cite link.
+Checks for pdf and doi, and add appropriate functions."
+ (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")]]
projects / org-ref.git / blobdiff