'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)
+
+
+(defcustom org-ref-insert-cite-function
+ 'org-ref-insert-cite-link
+ "Function to call to insert citation links."
+ :type 'function)
+
+
+(defcustom org-ref-cite-onclick-function
+ 'org-ref-cite-onclick-minibuffer-menu
+ "Function that runs when you click on a cite link. The function must take no arguments"
+ :type 'function)
#+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.
)
(make-local-variable 'reftex-cite-format)
(setq reftex-cite-format 'org)
- (define-key org-mode-map (kbd org-ref-insert-cite-key) 'org-ref-insert-cite-link))
+ (define-key org-mode-map (kbd org-ref-insert-cite-key) org-ref-insert-cite-function))
(add-hook 'org-mode-hook 'org-mode-reftex-setup)
(interactive)
(let* ((results (org-ref-get-bibtex-key-and-file))
(key (car results))
- (bibfile (cdr results)))
+ (bibfile (cdr results))
+ doi)
(save-excursion
(with-temp-buffer
(insert-file-contents bibfile)
(bibtex-search-entry key)
- (bibtex-autokey-get-field "doi")
+ (setq doi (bibtex-autokey-get-field "doi"))
;; in case doi is a url, remove the url part.
(replace-regexp-in-string "^http://dx.doi.org/" "" doi)))))
(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
(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 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))
(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."
+ (let* ((object (org-element-context)))
+ (cond
+ ;; case where we are in a link
+ ((and (equal (org-element-type object) 'link)
+ (-contains? org-ref-cite-types (org-element-property :type object)))
+ (goto-char 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))
+ (insert (concat "," (mapconcat 'identity keys ","))))
+
+ ;; We are next to a link, and we want to append
+ ((save-excursion
+ (backward-char)
+ (and (equal (org-element-type (org-element-context)) 'link)
+ (-contains? org-ref-cite-types (org-element-property :type (org-element-context)))))
+ (while (looking-back " ") (backward-char))
+ (insert (concat "," (mapconcat 'identity keys ","))))
+
+ ;; insert fresh link
+ (t
+ (insert
+ (concat org-ref-default-citation-link
+ ":"
+ (s-join keys ",")))))))
+
+(setq helm-bibtex-format-citation-functions
+ '((org-mode . helm-bibtex-format-org-ref)))
+
+(setq org-ref-insert-cite-function 'helm-bibtex)
+
+(require 'helm-bibtex)
+#+END_SRC
+
+** A helm click menu
+
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(defun test ()
+ (interactive)
+ (let* ((results (org-ref-get-bibtex-key-and-file))
+ (key (car results))
+ (bibfile (cdr results)))
+ (save-excursion
+ (with-temp-buffer
+ (insert-file-contents bibfile)
+ (bibtex-search-entry key)
+ (org-ref-bib-citation)))))
+
+(defun org-ref-cite-candidates ()
+ "Generate the list of possible candidates.
+Check 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 `( ;;the first candidate is a brief summary
+ (,(save-excursion
+ (with-temp-buffer
+ (insert-file-contents bibfile)
+ (bibtex-search-entry key))
+ (org-ref-bib-citation)) . org-ref-citation-at-point)
+ ("Open bibtex entry" . org-ref-open-citation-at-point))))
+
+ (message-box "doi = \"%s\"" doi)
+ (when (file-exists-p pdf-file)
+ (add-to-list
+ 'candidates
+ '("Open pdf" . org-ref-open-pdf-at-point)
+ t
+ ))
+
+ (add-to-list
+ 'candidates
+ '("Open notes" . org-ref-open-notes-at-point)
+ t)
+
+ (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" . (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)))))
+
+(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 (test))
+ (candidates (org-ref-cite-candidates))
+ (cb (current-buffer)))
+
+ (helm :sources `(((name . ,name)
+ (candidates . ,candidates)
+ (action . (lambda (f)
+ (switch-to-buffer cb)
+ (funcall f))))
+ ))))
+
+(setq org-ref-cite-onclick-function 'org-ref-cite-click-helm)
+#+END_SRC
+
+#+RESULTS:
+: org-ref-cite-click-helm
+
* End of code
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(provide 'org-ref)
projects / org-ref.git / blobdiff