(let* ((bibfile)
;; object is the link you clicked on
(object (org-element-context))
-
(link-string-beginning)
(link-string-end))
#+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)))
+ (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"
(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
+(defun org-ref-helm-insert-label-link ()
+ "Insert a label link. helm just shows you what labels already exist."
+ (interactive)
+ (let* ((labels (org-ref-get-labels))
+ (cb (current-buffer)))
+ (helm :sources `(((name . "Existing labels")
+ (candidates . ,labels)
+ (action . (lambda (label)
+ ;; unfortunately I do not have markers here
+ (org-open-link-from-string (format "ref:%s" label)))))
+ ((name . "Create new label")
+ (dummy)
+ (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.
#+BEGIN_SRC emacs-lisp :tangle org-ref.el
(insert (org-ref-complete-link)))
#+END_SRC
+Another alternative ref insertion is to use helm.
+
+#+BEGIN_SRC emacs-lisp
+(defun org-ref-helm-insert-ref-link ()
+ "Helm menu to insert ref links to labels in the document.
+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 :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)))
+ (action . (lambda (label)
+ (switch-to-buffer ,cb)
+ (insert
+ (concat
+ (if helm-current-prefix-arg
+ (helm :sources '((name . "Ref link types")
+ (candidates . ("ref" "eqref" "pageref" "nameref"))
+ (action . (lambda (x) x))))
+ "ref")
+ ":" label)))))))))
+#+END_SRC
+
+#+RESULTS:
+: org-ref-helm-insert-ref-link
+
** pageref
This refers to the page of a label in LaTeX.
(format "\\Glspl{%s}" path)))))
#+END_SRC
-
* Utilities
** create simple text citation from bibtex entry
#+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
(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.
(point))
(progn
(forward-line 4)
- (point))))))))
+ (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 ()
(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"))))))))))
+ "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
#+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."
+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)))
(cond
;; case where we are in a link
(-contains?
org-ref-cite-types
(org-element-property :type object)))
- ;;(message-box "in a link")
- (goto-char (org-element-property :end object))
- ;; 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 ","))))
+ (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.
+ " ")))
+ (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.
(t
;;(message-box "fresh link")
(insert
- (concat (if helm-current-prefix-arg
+ (concat (if (equal helm-current-prefix-arg '(4))
(helm :sources `((name . "link types")
(candidates . ,org-ref-cite-types)
(action . (lambda (x) x))))
(helm-bibtex)))
(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
(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)))))
+ (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.
projects / org-ref.git / blobdiff