** Header
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-;;; org-ref.el --- setup bibliography, cite, ref and label org-mode links.
+;;; org-ref.el --- cite and cross-reference in org-mode
;; Copyright(C) 2014 John Kitchin
;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
+;; URL: https://github.com/jkitchin/org-ref
+;; Version: 0.1
+;; Keywords: org-mode, cite, ref, label
+;; Package-Requires: ((dash) (helm) (helm-bibtex))
+
;; This file is not currently part of GNU Emacs.
;; This program is free software; you can redistribute it and/or
;;; Commentary:
;;
-;; 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.
+;; 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) (helm) (helm-bibtex))
+
+;;; Code:
#+END_SRC
** requires
(require 'helm)
(require 'helm-config)
(require 'helm-bibtex)
+(require 'org)
#+END_SRC
** Custom variables
We create the links by mapping the function onto the list of defined link types.
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+;;;###autoload
(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 ::."
+ "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]]."
(interactive)
(cond
((string-match "::" desc)
(format "[%s][%s]" (car (setq results (split-string desc "::"))) (cadr results)))
(t (format "[%s]" desc))))
+;;;###autoload
(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.
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+;;;###autoload
(defun org-ref-insert-cite-link (alternative-cite)
"Insert a default citation link using reftex. If you are on a link, it
appends to the end of the link, otherwise, a new link is
(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
Alternatively, you may shortcut the org-machinery with this command. You will be prompted for a citation type, and then offered key completion.
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+;;;###autoload
(defun org-ref-insert-cite-with-completion (type)
"Insert a cite link with completion"
(interactive (list (ido-completing-read "Type: " org-ref-cite-types)))
org-mode already defines a store link function for bibtex entries. It does not store the link I want though, it only stores a brief citation of the entry. I want a citation link. Here is a function to do that.
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+;;;###autoload
(defun org-ref-store-bibtex-entry-link ()
"Save a citation link to the current bibtex entry. Saves in the default link type."
(interactive)
** open pdf from bibtex
We bind this to a key here: [[*key%20bindings%20for%20utilities][key bindings for utilities]].
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+;;;###autoload
(defun org-ref-open-bibtex-pdf ()
"open pdf for a bibtex entry, if it exists. assumes point is in
the entry of interest in the bibfile. but does not check that."
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)
+;;;###autoload
(defun org-ref-swap-citation-link (direction)
"move citation at point in direction +1 is to the right, -1 to the left"
(interactive)
(point)))))
(throw 'result "!!! NO CONTEXT FOUND !!!"))))
-
+;;;###autoload
(defun org-ref-link-message ()
"Print a minibuffer message about the link that point is on."
(interactive)
(setq helm-bibtex-additional-search-fields '(keywords))
#+END_SRC
-Next, we are going to add keywords to the helm interface.
+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
(defun helm-bibtex-candidates-formatter (candidates source)
"Formats BibTeX entries for display in results list."
#+END_SRC
-1. Make the default action to insert selected keys.
-2. Make open entry second action
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+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
+;; adapted from bibtex-utils.el
+;; these are candidates for selecting keywords/tags
+(defun org-ref-bibtex-keywords ()
+ "Get keywords defined in current bibtex file.
+These are in the keywords field, and are comma or semicolon separated."
+ (save-excursion
+ (goto-char (point-min))
+ (let (keywords kstring)
+ (while (re-search-forward "^\\s-*keywords.*{\\([^}]+\\)}" nil t)
+ ;; TWS - remove newlines/multiple spaces:
+ (setq kstring (replace-regexp-in-string "[ \t\n]+" " " (match-string 1)))
+ (mapc
+ (lambda (v)
+ (add-to-list 'keywords v t))
+ (split-string kstring "\\(,\\|;\\)[ \n]*\\|{\\|}" t)))
+ keywords)))
+
+;;;###autoload
+(defun org-ref-set-bibtex-keywords (keywords &optional arg)
+ "Add KEYWORDS to a bibtex entry.
+If KEYWORDS is a list, it is converted to a comma-separated string. The KEYWORDS are added to the beginning of the field. Otherwise KEYWORDS should be a string of comma-separate keywords."
+ (interactive "sKeywords: \nP")
+ (bibtex-set-field
+ "keywords"
+ (if arg
+ ;; replace with arg
+ (if (listp keywords)
+ (mapconcat 'identity keywords ", ")
+ keywords)
+ ;; else concatentate
+ (concat
+ (if (listp keywords)
+ (mapconcat 'identity keywords ", ")
+ keywords)
+ (when (not (string= "" (bibtex-autokey-get-field "keywords")))
+ (concat ", " (bibtex-autokey-get-field "keywords"))))))
+ (save-buffer))
+
+;;;###autoload
+(defun helm-tag-bibtex-entry ()
+ "Helm interface to add keywords to a bibtex entry.
+Run this with the point in a bibtex entry."
+ (interactive)
+ (let ((keyword-source `((name . "Existing keywords")
+ (candidates . ,(org-ref-bibtex-keywords))
+ (action . (lambda (candidate)
+ (org-ref-set-bibtex-keywords
+ (mapconcat
+ 'identity
+ (helm-marked-candidates)
+ ", "))))))
+ (fallback-source `((name . "Add new keywords")
+ (dummy)
+ (action . (lambda (candidate)
+ (org-ref-set-bibtex-keywords helm-pattern)
+ )))))
+ (helm :sources '(keyword-source fallback-source))))
+
+
(defun org-ref-helm-tag-entries (candidates)
- "Set tags on selected bibtex entries from helm.
-User is prompted for tags."
+ "Set tags on selected bibtex entries from helm-bibtex.
+User is prompted for tags. This function is called from `helm-bibtex'."
(let ((keywords (read-input "Keywords (comma separated): ")))
(loop for key in (helm-marked-candidates)
do
"keywords"
(concat
keywords
- "," (bibtex-autokey-get-field "keywords")))
+ ", " (bibtex-autokey-get-field "keywords")))
(save-buffer)))))
+#+END_SRC
+
+Next, adapt the helm-bibtex source with these features:
+
+1. Make the default action to insert selected keys.
+2. Make open entry second action
+3. Add some features for adding keywords to bibtex entries.
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(setq helm-source-bibtex
'((name . "BibTeX entries")
(init . helm-bibtex-init)
(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.
#+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))
'org-ref-helm-user-candidates
'("Example" . (lambda () (message-box "You did it!")))
t)
-
+;;;###autoload
(defun org-ref-cite-click-helm (key)
"subtle points.
1. get name and candidates before entering helm because we need the org-buffer.
* End of code
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(provide 'org-ref)
+
+;;; org-ref.el ends here
#+END_SRC
* Build :noexport:
projects / org-ref.git / blobdiff