+# -*- org-edit-src-content-indentation: 0; -*-
#+TITLE: Org-ref - The best reference handling for org-mode
#+AUTHOR: John Kitchin
#+DATE: April 29, 2014
(require 'helm)
(require 'helm-config)
(require 'helm-bibtex)
+(require 'org)
#+END_SRC
** Custom variables
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))
(link-string (org-element-property :path object)))
;; you may click on the part before the citations. here we make
falling back to what the user has set in org-ref-default-bibliography
"
- (interactive)
(catch 'result
(save-excursion
(goto-char (point-min))
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-ref-get-bibtex-key-and-file (&optional key)
"returns the bibtex key and file that it is in. If no key is provided, get one under point"
- (interactive)
(let ((org-ref-bibliography-files (org-ref-find-bibliography))
(file))
(unless key
(defun org-ref-get-doi-at-point ()
"Get doi for key at point."
- (interactive)
(let* ((results (org-ref-get-bibtex-key-and-file))
(key (car results))
(bibfile (cdr results))
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-ref-format-citation-description (desc)
- "return formatted citation description. if the cite link has a description, it is optional text for the citation command. You can specify pre and post text by separating these with ::."
- (interactive)
+ "Return formatted citation description. If the cite link has a
+description, it is optional text for the citation command. You
+can specify pre and post text by separating these with ::, for
+example [[cite:key][pre text::post text]]."
(cond
((string-match "::" desc)
(format "[%s][%s]" (car (setq results (split-string desc "::"))) (cadr results)))
(t (format "[%s]" 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:
+ "Add a citation link of TYPE 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,
and the completion function."
(interactive "sCitation Type: \ncKey: ")
(mapcar 'org-ref-define-citation-link org-ref-cite-types)
#+END_SRC
+#+RESULTS:
+
*** org-ref-insert-cite-link
We need a convenient method to insert links. In reftex you use the keystroke C-c ], which gives you a minibuffer to search the bibtex files from. This function is bound to that same keystroke here [[*org-mode%20/%20reftex%20setup][org-mode / reftex setup]]. This function will append to a cite link if you call it while on a link.
(mapconcat 'identity (reftex-citation t) ",")))))
;; you pressed a C-u so we run this code
- (reftex-citation)))
- )
+ (reftex-citation))))
#+END_SRC
cite:zhou-2004-first-lda-u,paier-2006-errat,boes-2015-estim-bulk
(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))
- (message-box "%s" link)
(setq
bad-citations
(append
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
+;;;###autoload
(defun org-ref ()
"Opens a helm interface to actions for org-ref.
Shows bad citations, ref links and labels"
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-ref-get-citation-year (key)
"get the year of an entry with key. Returns year as a string."
- (interactive)
(let* ((results (org-ref-get-bibtex-key-and-file key))
(bibfile (cdr results)))
(with-temp-buffer
))))
(defun org-ref-sort-citation-link ()
- "replace link at point with sorted link by year"
+ "Replace link at point with sorted link by year."
(interactive)
(let* ((object (org-element-context))
(type (org-element-property :type object))
Sometimes it may be helpful to manually change the order of citations. These functions define shift-arrow functions.
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun org-ref-swap-keys (i j keys)
- "swap the keys in a list with index i and j"
+ "Swap the KEYS in a list with index I and J."
(let ((tempi (nth i keys)))
(setf (nth i keys) (nth j keys))
(setf (nth j keys) tempi))
keys)
+
(defun org-ref-swap-citation-link (direction)
"move citation at point in direction +1 is to the right, -1 to the left"
(interactive)
(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
+ ;; It seems the space at the end can get consumed, so we see if there
+ ;; is a space, and add it if so. Sometimes there is a comma or period,
+ ;; then we do not want a space.
+ (when
+ (save-excursion
+ (goto-char end)
+ (looking-back " ")) " ")))
;; now go forward to key so we can move with the key
(re-search-forward key)
(goto-char (match-beginning 0)))))
[[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.
Let us add keywords as a searchable field.
-#+BEGIN_SRC emacs-lisp
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(setq helm-bibtex-additional-search-fields '(keywords))
#+END_SRC
Next, we are going to add keywords to the helm interface. This modifies the helm-bibtex function to add our keywords.
-#+BEGIN_SRC emacs-lisp
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(defun helm-bibtex-candidates-formatter (candidates source)
"Formats BibTeX entries for display in results list."
(cl-loop
- with width = (with-helm-window (window-width))
- for entry in candidates
- for entry = (cdr entry)
- for entry-key = (helm-bibtex-get-value entry 'entry-key)
- for fields = (--map (helm-bibtex-clean-string
- (helm-bibtex-get-value entry it " "))
- '(author title year has-pdf has-note entry-type))
- for fields = (-update-at 0 'helm-bibtex-shorten-authors fields)
- for fields = (append fields
- (list (or (helm-bibtex-get-value entry 'keywords)
+ with width = (with-helm-window (helm-bibtex-window-width))
+ for entry in candidates
+ for entry = (cdr entry)
+ for entry-key = (helm-bibtex-get-value "=key=" entry)
+ if (assoc-string "author" entry 'case-fold)
+ for fields = '("author" "title" "year" "=has-pdf=" "=has-note=" "=type=")
+ else
+ for fields = '("editor" "title" "year" "=has-pdf=" "=has-note=" "=type=")
+ for fields = (--map (helm-bibtex-clean-string
+ (helm-bibtex-get-value it entry " "))
+ fields)
+ for fields = (-update-at 0 'helm-bibtex-shorten-authors fields)
+ for fields = (append fields
+ (list (or (helm-bibtex-get-value "keywords" entry)
"" )))
- collect
- (cons (s-format "$0 $1 $2 $3 $4$5 $6" 'elt
- (-zip-with (lambda (f w) (truncate-string-to-width f w 0 ?\s))
- fields (list 36 (- width 85) 4 1 1 7 7)))
- entry-key)))
-
+ collect
+ (cons (s-format "$0 $1 $2 $3 $4$5 $6" 'elt
+ (-zip-with (lambda (f w) (truncate-string-to-width f w 0 ?\s))
+ fields (list 36 (- width 85) 4 1 1 7 7)))
+ entry-key)))
#+END_SRC
Next, we add some functions to add keywords to a bibtex entry using a helm interface, and a new action to add keywords to entries from helm-bibtex.
-#+BEGIN_SRC emacs-lisp
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
;; adapted from bibtex-utils.el
;; these are candidates for selecting keywords/tags
(defun org-ref-bibtex-keywords ()
)))))
(helm :sources '(keyword-source fallback-source))))
+(defun helm-bibtex-show-entry (key)
+ "Show the entry in the BibTeX file.
+The original function in helm-bibtex has a bug where it finds the
+first key that partially matches. This version avoids that."
+ (catch 'break
+ (dolist (bibtex-file (if (listp helm-bibtex-bibliography)
+ helm-bibtex-bibliography
+ (list helm-bibtex-bibliography)))
+ (let ((buf (helm-bibtex-buffer-visiting bibtex-file))
+ (entries '()))
+ (find-file bibtex-file)
+ (bibtex-map-entries
+ (lambda (key start end)
+ (add-to-list 'entries (cons key start))))
+ (if (assoc key entries)
+ (progn
+ (goto-char (cdr (assoc key entries)))
+ (throw 'break t))
+ (unless buf
+ (kill-buffer)))))))
(defun org-ref-helm-tag-entries (candidates)
"Set tags on selected bibtex entries from helm-bibtex.
User is prompted for tags. This function is called from `helm-bibtex'."
+ (message "")
(let ((keywords (read-input "Keywords (comma separated): ")))
(loop for key in (helm-marked-candidates)
do
(setq helm-bibtex-format-citation-functions
'((org-mode . helm-bibtex-format-org-ref)))
+;;;###autoload
(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.
((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
#+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)))
(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))
'("Example" . (lambda () (message-box "You did it!")))
t)
+;;;###autoload
(defun org-ref-cite-click-helm (key)
- "subtle points.
+ "Open helm for actions on a cite link.
+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)
projects / org-ref.git / blobdiff