-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
-(defun org-ref-insert-cite-with-completion (type)
- "Insert a cite link with completion"
- (interactive (list (ido-completing-read "Type: " org-ref-cite-types)))
- (insert (funcall (intern (format "org-%s-complete-link" type)))))
-#+END_SRC
-
-** Storing links to a bibtex entry
-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
-(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
- ":"
- (save-excursion
- (bibtex-beginning-of-entry)
- (reftex-get-bib-field "=key=" (bibtex-parse-entry))))))
- (message "saved %s" link)
- (push (list link) org-stored-links)
- (car org-stored-links)))
-#+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."
-
- (bibtex-beginning-of-entry)
- (let* ((cb (current-buffer))
- (bibtex-expand-strings t)
- (entry (loop for (key . value) in (bibtex-parse-entry t)
- collect (cons (downcase key) value)))
- (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
- (year (reftex-get-bib-field "year" entry))
- (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
- (key (reftex-get-bib-field "=key=" entry))
- (journal (reftex-get-bib-field "journal" entry))
- (volume (reftex-get-bib-field "volume" entry))
- (pages (reftex-get-bib-field "pages" entry))
- (doi (reftex-get-bib-field "doi" entry))
- (url (reftex-get-bib-field "url" entry))
- )
- ;;authors, "title", Journal, vol(iss):pages (year).
- (format "%s, \"%s\", %s, %s:%s (%s)"
- author title journal volume pages year)))
-#+END_SRC
-
-#+RESULTS:
-: org-ref-bib-citation
-
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-bib-html-citation ()
- "from a bibtex entry, create and return a simple citation with html links."
-
- (bibtex-beginning-of-entry)
- (let* ((cb (current-buffer))
- (bibtex-expand-strings t)
- (entry (loop for (key . value) in (bibtex-parse-entry t)
- collect (cons (downcase key) value)))
- (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
- (year (reftex-get-bib-field "year" entry))
- (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
- (key (reftex-get-bib-field "=key=" entry))
- (journal (reftex-get-bib-field "journal" entry))
- (volume (reftex-get-bib-field "volume" entry))
- (pages (reftex-get-bib-field "pages" entry))
- (doi (reftex-get-bib-field "doi" entry))
- (url (reftex-get-bib-field "url" entry))
- )
- ;;authors, "title", Journal, vol(iss):pages (year).
- (concat (format "%s, \"%s\", %s, %s:%s (%s)."
- author title journal volume pages year)
- (when url (format " <a href=\"%s\">link</a>" url))
- (when doi (format " <a href=\"http://dx.doi.org/%s\">doi</a>" doi)))
- ))
-#+END_SRC
-
-** 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
-(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."
- (interactive)
- (save-excursion
- (bibtex-beginning-of-entry)
- (let* ((bibtex-expand-strings t)
- (entry (bibtex-parse-entry t))
- (key (reftex-get-bib-field "=key=" entry))
- (pdf (format (concat org-ref-pdf-directory "%s.pdf") key)))
- (message "%s" pdf)
- (if (file-exists-p pdf)
- (org-open-link-from-string (format "[[file:%s]]" pdf))
- (ding)))))
-#+END_SRC
-
-** open notes 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
-(defun org-ref-open-bibtex-notes ()
- "from a bibtex entry, open the notes if they exist, and create a heading if they do not.
-
-I never did figure out how to use reftex to make this happen
-non-interactively. the reftex-format-citation function did not
-work perfectly; there were carriage returns in the strings, and
-it did not put the key where it needed to be. so, below I replace
-the carriage returns and extra spaces with a single space and
-construct the heading by hand."
- (interactive)
-
- (bibtex-beginning-of-entry)
- (let* ((cb (current-buffer))
- (bibtex-expand-strings t)
- (entry (loop for (key . value) in (bibtex-parse-entry t)
- collect (cons (downcase key) value)))
- (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
- (year (reftex-get-bib-field "year" entry))
- (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
- (key (reftex-get-bib-field "=key=" entry))
- (journal (reftex-get-bib-field "journal" entry))
- (volume (reftex-get-bib-field "volume" entry))
- (pages (reftex-get-bib-field "pages" entry))
- (doi (reftex-get-bib-field "doi" entry))
- (url (reftex-get-bib-field "url" entry))
- )
-
- ;; save key to clipboard to make saving pdf later easier by pasting.
- (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-other-window org-ref-bibliography-notes)
- (error "org-ref-bib-bibliography-notes is not set to anything"))
-
- (goto-char (point-min))
- ;; put new entry in notes if we don't find it.
- (if (re-search-forward (format ":Custom_ID: %s$" key) nil 'end)
- (funcall org-ref-open-notes-function)
- ;; no entry found, so add one
- (insert (format "\n** TODO %s - %s" year title))
- (insert (format"
- :PROPERTIES:
- :Custom_ID: %s
- :AUTHOR: %s
- :JOURNAL: %s
- :YEAR: %s
- :VOLUME: %s
- :PAGES: %s
- :DOI: %s
- :URL: %s
- :END:
-[[cite:%s]] [[file:%s/%s.pdf][pdf]]\n\n"
-key author journal year volume pages doi url key org-ref-pdf-directory key))
-(save-buffer))))
-#+END_SRC
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-open-notes-from-reftex ()
- "Call reftex, and open notes for selected entry."
- (interactive)
- (let ((bibtex-key )))
-
- ;; now look for entry in the notes file
- (if org-ref-bibliography-notes
- (find-file-other-window org-ref-bibliography-notes)
- (error "org-ref-bib-bibliography-notes is not set to anything"))
-
- (goto-char (point-min))
-
- (re-search-forward (format
- ":Custom_ID: %s$"
- (first (reftex-citation t)) nil 'end))
- (funcall org-ref-open-notes-function))
-#+END_SRC
-
-** open url in browser from bibtex
-
-We bind this to a key here [[*key%20bindings%20for%20utilities][key bindings for utilities]].
-
-+ This function may be duplicative of bibtex-url. But I think my function is better unless you do some complicated customization of bibtex-generate-url-list.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-open-in-browser ()
- "Open the bibtex entry at point in a browser using the url field or doi field"
-(interactive)
-(save-excursion
- (bibtex-beginning-of-entry)
- (catch 'done
- (let ((url (bibtex-autokey-get-field "url")))
- (when url
- (browse-url url)
- (throw 'done nil)))
-
- (let ((doi (bibtex-autokey-get-field "doi")))
- (when doi
- (if (string-match "^http" doi)
- (browse-url doi)
- (browse-url (format "http://dx.doi.org/%s" doi)))
- (throw 'done nil)))
- (message "No url or doi found"))))
-#+END_SRC
-
-** citeulike
- I discovered you could upload a bibtex entry to citeulike using http requests. The upload is actually done by a [[*The%20upload%20script][python script]], because it was easy to write. Here is the emacs command to do this. It is not a fast operation, and do not use it frequently.
-
-*** function to upload bibtex to citeulike
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-upload-bibtex-entry-to-citeulike ()
- "with point in a bibtex entry get bibtex string and submit to citeulike.
-
-Relies on the python script /upload_bibtex_citeulike.py being in the user directory."
- (interactive)
- (message "uploading to citeulike")
- (save-restriction
- (bibtex-narrow-to-entry)
- (let ((startpos (point-min))
- (endpos (point-max))
- (bibtex-string (buffer-string))
- (script (concat "python " starter-kit-dir "/upload_bibtex_citeulike.py&")))
- (with-temp-buffer (insert bibtex-string)
- (shell-command-on-region (point-min) (point-max) script t nil nil t)))))
-#+END_SRC
-
-*** The upload script
-Here is the python script for uploading.
-
-*************** TODO document how to get the cookies
-*************** END
-
-
-#+BEGIN_SRC python :tangle upload_bibtex_citeulike.py
-#!python
-import pickle, requests, sys
-
-# reload cookies
-with open('c:/Users/jkitchin/Dropbox/blogofile-jkitchin.github.com/_blog/cookies.pckl', 'rb') as f:
- cookies = pickle.load(f)
-
-url = 'http://www.citeulike.org/profile/jkitchin/import_do'
-
-bibtex = sys.stdin.read()
-
-data = {'pasted':bibtex,
- 'to_read':2,
- 'tag_parsing':'simple',
- 'strip_brackets':'no',
- 'update_id':'bib-key',
- 'btn_bibtex':'Import BibTeX file ...'}
-
-headers = {'content-type': 'multipart/form-data',
- 'User-Agent':'jkitchin/johnrkitchin@gmail.com bibtexupload'}
-
-r = requests.post(url, headers=headers, data=data, cookies=cookies, files={})
-print r
-#+END_SRC
-
-** Build a pdf from a bibtex file
- It is useful to have a pdf version of an entire bibliography to check it for formatting, spelling, or to share it. This function creates a pdf from a bibtex file. I only include the packages I commonly use in my bitex files.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-build-full-bibliography ()
- "build pdf of all bibtex entries, and open it."
- (interactive)
- (let* ((bibfile (file-name-nondirectory (buffer-file-name)))
- (bib-base (file-name-sans-extension bibfile))
- (texfile (concat bib-base ".tex"))
- (pdffile (concat bib-base ".pdf")))
- (find-file texfile)
- (erase-buffer)
- (insert (format "\\documentclass[12pt]{article}
-\\usepackage[version=3]{mhchem}
-\\usepackage{url}
-\\usepackage[numbers]{natbib}
-\\usepackage[colorlinks=true, linkcolor=blue, urlcolor=blue, pdfstartview=FitH]{hyperref}
-\\usepackage{doi}
-\\begin{document}
-\\nocite{*}
-\\bibliographystyle{unsrtnat}
-\\bibliography{%s}
-\\end{document}" bib-base))
- (save-buffer)
- (shell-command (concat "pdflatex " bib-base))
- (shell-command (concat "bibtex " bib-base))
- (shell-command (concat "pdflatex " bib-base))
- (shell-command (concat "pdflatex " bib-base))
- (kill-buffer texfile)
- (org-open-file pdffile)
- ))
-#+END_SRC
-
-** Extract bibtex entries cited in an org-file
-When you use your default bibliography file, and you want to send an org-file to a collaborator, you may need to include bibtex entries so the other person can see them. This function does that and puts the entries in a section at the end of the document that can be tangled to a bib-file.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-extract-bibtex-entries ()
- "extract the bibtex entries referred to by cite links in the current buffer into a src block at the bottom of the current buffer.
-
-If no bibliography is in the buffer the `reftex-default-bibliography' is used."
- (interactive)
- (let* ((temporary-file-directory (file-name-directory (buffer-file-name)))
- (tempname (make-temp-file "extract-bib"))
- (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
- (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"
- (mapconcat 'identity reftex-default-bibliography ",")))))
- (save-buffer)
-
- ;; get a latex file and extract the references
- (org-latex-export-to-latex)
- (find-file texfile)
- (reftex-parse-all)
- (reftex-create-bibtex-file bibfile)
- (save-buffer)
- ;; save results of the references
- (setq results (buffer-string))
-
- ;; kill buffers. these are named by basename, not full path
- (kill-buffer (concat basename ".bib"))
- (kill-buffer (concat basename ".tex"))
- (kill-buffer basename)
-
- (delete-file bibfile)
- (delete-file texfile)
- (delete-file tempname)
-
- ;; Now back to the original org buffer and insert the results
- (switch-to-buffer cb)
- (when (not (string= "" results))
- (save-excursion
- (goto-char (point-max))
- (insert "\n\n")
- (org-insert-heading)
- (insert (format " Bibtex entries
-
-,#+BEGIN_SRC text :tangle %s
-%s
-,#+END_SRC" (concat (file-name-sans-extension (file-name-nondirectory (buffer-file-name))) ".bib") results))))))
-#+END_SRC
-
-** Find bad cite links
-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
-(require 'cl)
-
-(defun index (substring list)
- "return the index of string in a list of strings"
- (let ((i 0)
- (found nil))
- (dolist (arg list i)
- (if (string-match (concat "^" substring "$") arg)
- (progn
- (setq found t)
- (return i)))
- (setq i (+ i 1)))
- ;; return counter if found, otherwise return nil
- (if found i nil)))
-
-
-(defun org-ref-find-bad-citations ()
- "Create a list of citation keys in an org-file that do not have a bibtex entry in the known bibtex files.
-
-Makes a new buffer with clickable links."
- (interactive)
- ;; generate the list of bibtex-keys and cited keys
- (let* ((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 (equal (plist-get plist ':type) "cite")
- (dolist (key (org-ref-split-and-strip-string (plist-get plist ':path)) )
- (when (not (index key bibtex-keys))
- (setq bad-citations (append bad-citations
- `(,(format "%s [[elisp:(progn (switch-to-buffer-other-frame \"%s\")(goto-char %s))][not found here]]\n"
- key (buffer-name)(plist-get plist ':begin)))))
- ))))))
-
- (if bad-citations
- (progn
- (switch-to-buffer-other-window "*Missing citations*")
- (org-mode)
- (erase-buffer)
- (insert "* List of bad cite links\n")
- (insert (mapconcat 'identity bad-citations ""))
- ;(setq buffer-read-only t)
- (use-local-map (copy-keymap org-mode-map))
- (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))
-
- (when (get-buffer "*Missing citations*")
- (kill-buffer "*Missing citations*"))
- (message "No bad cite links found"))))
-#+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.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-find-non-ascii-characters ()
- "finds non-ascii characters in the buffer. Useful for cleaning up bibtex files"
- (interactive)
- (occur "[^[:ascii:]]"))
-#+END_SRC
-
-** Resort a bibtex entry
-I like neat and orderly bibtex entries.That means the fields are in a standard order that I like. This function reorders the fields in an entry for articles, and makes sure the fields are in lowercase.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-sort-bibtex-entry ()
- "sort fields of entry in standard order and downcase them"
- (interactive)
- (bibtex-beginning-of-entry)
- (let* ((master '("author" "title" "journal" "volume" "number" "pages" "year" "doi" "url"))
- (entry (bibtex-parse-entry))
- (entry-fields)
- (other-fields)
- (type (cdr (assoc "=type=" entry)))
- (key (cdr (assoc "=key=" entry))))
-
- ;; these are the fields we want to order that are in this entry
- (setq entry-fields (mapcar (lambda (x) (car x)) entry))
- ;; we do not want to reenter these fields
- (setq entry-fields (remove "=key=" entry-fields))
- (setq entry-fields (remove "=type=" entry-fields))
-
- ;;these are the other fields in the entry
- (setq other-fields (remove-if-not (lambda(x) (not (member x master))) entry-fields))
-
- (cond
- ;; right now we only resort articles
- ((string= (downcase type) "article")
- (bibtex-kill-entry)
- (insert
- (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)
- (format "%s = %s," (downcase field) (cdr (assoc field entry)))) other-fields "\n")
- "\n}\n\n"))
- (bibtex-find-entry key)
- (bibtex-fill-entry)
- (bibtex-clean-entry)
- ))))
-#+END_SRC
-
-** Clean a bibtex entry
- I like neat and orderly bibtex entries. This code will eventually replace the key with my style key, clean the entry, and sort the fields in the order I like them.
-see [[file:emacs-24.3/lisp/textmodes/bibtex.el::bibtex-autokey-before-presentation-function]] for how to set a function that checks for uniqueness of the key.
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(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)
-(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))
- (end-of-line)
- (insert ","))
-
- ;; check for empty pages, and put eid or article id in its place
- (let ((entry (bibtex-parse-entry))
- (pages (bibtex-autokey-get-field "pages"))
- (year (bibtex-autokey-get-field "year"))
- (doi (bibtex-autokey-get-field "doi"))
- ;; The Journal of Chemical Physics uses eid
- (eid (bibtex-autokey-get-field "eid")))
-
- ;; replace http://dx.doi.org/ in doi. some journals put that in,
- ;; but we only want the doi.
- (when (string-match "^http://dx.doi.org/" doi)
- (bibtex-beginning-of-entry)
- (goto-char (car (cdr (bibtex-search-forward-field "doi" t))))
- (bibtex-kill-field)
- (bibtex-make-field "doi")
- (backward-char)
- (insert (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))
-
- ;; asap articles often set year to 0, which messes up key
- ;; generation. fix that.
- (when (string= "0" year)
- (bibtex-beginning-of-entry)
- (goto-char (car (cdr (bibtex-search-forward-field "year" t))))
- (bibtex-kill-field)
- (bibtex-make-field "year")
- (backward-char)
- (insert (read-string "Enter year: ")))
-
- ;; fix pages if they are empty if there is an eid to put there.
- (when (string= "-" pages)
- (when eid
- (bibtex-beginning-of-entry)
- ;; this seems like a clunky way to set the pages field.But I
- ;; cannot find a better way.
- (goto-char (car (cdr (bibtex-search-forward-field "pages" t))))
- (bibtex-kill-field)
- (bibtex-make-field "pages")
- (backward-char)
- (insert eid)))
-
- ;; replace naked & with \&
- (save-restriction
- (bibtex-narrow-to-entry)
- (bibtex-beginning-of-entry)
- (message "checking &")
- (replace-regexp " & " " \\\\& ")
- (widen))
-
- ;; generate a key, and if it duplicates an existing key, edit it.
- (unless keep-key
- (let ((key (bibtex-generate-autokey)))
-
- ;; first we delete the existing key
- (bibtex-beginning-of-entry)
- (re-search-forward bibtex-entry-maybe-empty-head)
- (if (match-beginning bibtex-key-in-head)
- (delete-region (match-beginning bibtex-key-in-head)
- (match-end bibtex-key-in-head)))
- ;; check if the key is in the buffer
- (when (save-excursion
- (bibtex-search-entry key))
- (save-excursion
- (bibtex-search-entry key)
- (bibtex-copy-entry-as-kill)
- (switch-to-buffer-other-window "*duplicate entry*")
- (bibtex-yank))
- (setq key (bibtex-read-key "Duplicate Key found, edit: " key)))
-
- (insert key)
- (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.
- ;; (run-hooks org-ref-clean-bibtex-entry-hook)
- (mapcar (lambda (x)
- (save-restriction
- (save-excursion
- (funcall x))))
- org-ref-clean-bibtex-entry-hook)
-
- ;; sort fields within entry
- (org-ref-sort-bibtex-entry)
- ;; check for non-ascii characters
- (occur "[^[:ascii:]]")
- ))
-#+END_SRC
-
-#+RESULTS:
-: org-ref-clean-bibtex-entry
-
-** Sort the entries in a citation link by year
-I prefer citations in chronological order within a grouping. These functions sort the link under the cursor by year.
-
-#+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
- (insert-file-contents bibfile)
- (bibtex-search-entry key nil 0)
- (prog1 (reftex-get-bib-field "year" (bibtex-parse-entry t))
- ))))
-
-(defun org-ref-sort-citation-link ()
- "replace link at point with sorted link by year"
- (interactive)
- (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 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
- (setq keys (mapconcat (lambda (x) (cdr x)) data ","))
- ;; and replace the link with the sorted keys
- (cl--set-buffer-substring begin end (concat type ":" keys))))
-#+END_SRC
-
-** Sort entries in citation links with shift-arrow keys
-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"
- (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)
- (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))
- key keys i)
- ;; We only want this to work on citation links
- (when (-contains? org-ref-cite-types type)
- (setq key (org-ref-get-bibtex-key-under-cursor))
- (setq keys (org-ref-split-and-strip-string link-string))
- (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))
- (setq keys (mapconcat 'identity keys ","))
- ;; and replace the link with the sorted 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)
- (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
-* Aliases
-I like convenience. Here are some aliases for faster typing.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defalias 'oro 'org-ref-open-citation-at-point)
-(defalias 'orc 'org-ref-citation-at-point)
-(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 'orir 'org-ref-insert-ref-link)
-(defalias 'orsl 'org-ref-store-bibtex-entry-link)
-
-(defalias 'orcb 'org-ref-clean-bibtex-entry)
-#+END_SRC
-* End of code
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(provide 'org-ref)
-#+END_SRC
-
-
-* Build :noexport:
-
-[[elisp:(progn (org-babel-tangle) (load-file "org-ref.el"))]]
-
-[[elisp:(org-babel-load-file "org-ref.org")]]
-