X-Git-Url: https://git.donarmstrong.com/?p=org-ref.git;a=blobdiff_plain;f=org-ref.org;h=44aa74b7541844d857924bc3f64cd1fd6476c44c;hp=c59d8d10b60b79c78f03b16d84479a6a6767af02;hb=076d9bffd0ed994a5a7452799f72ea8ce8553537;hpb=1640b223fedc30e829bea58d949881d27894b572 diff --git a/org-ref.org b/org-ref.org index c59d8d1..44aa74b 100644 --- a/org-ref.org +++ b/org-ref.org @@ -12,6 +12,20 @@ This document is an experiment at creating a literate program to provide similar 4. Exportable links to LaTeX 5. Utility functions for dealing with bibtex files and org-files +Some additional features include +1. Get minibuffer messages for the cite/ref/label link under point + +With helm integration (default) you can: + +1. C-c ] to insert a citation link + in helm-bibtex + - Enter to insert or append citation(s) + - C-u Enter to insert an alternative cite link + - C-u C-u Enter to replace the citation at point +2. C-u C-c ] to insert a ref link with helm completion +3. C-u C-u C-c ] to insert a label with completion +4. M-x org-ref to get a helm completion buffer with link checks, utilities and export options + ** Header #+BEGIN_SRC emacs-lisp :tangle org-ref.el ;;; org-ref.el --- setup bibliography, cite, ref and label org-mode links. @@ -228,26 +242,6 @@ We setup reftex here. We use a custom insert cite link function defined here: [[ (kbd org-ref-insert-cite-key) org-ref-insert-cite-function) -(when org-ref-show-citation-on-enter - (setq org-ref-message-timer - (run-with-idle-timer 0.5 t 'org-ref-link-message))) - -(defun org-ref-show-link-messages () - "Turn on link messages. You will see a message in the -minibuffer when on a cite, ref or label link." - (interactive) - (setq org-ref-message-timer - (run-with-idle-timer 0.5 t 'org-ref-link-message)) - ) -(defun org-ref-cancel-link-messages () - "Stop showing messages in minibuffer when on a link." - (interactive) - (cancel-timer org-ref-message-timer)) - -;; this approach caused the selected region to not be highlighted any more. -; (add-hook 'post-command-hook 'org-ref-link-message)) -; (remove-hook 'post-command-hook 'org-ref-link-message)) - (add-hook 'org-mode-hook 'org-mode-reftex-setup) (eval-after-load 'reftex-vars @@ -283,6 +277,100 @@ You can define a new citation link like this: (org-ref-define-citation-link "citez" ?z) #+END_SRC +** Messages for link at cursor +Here we setup code that shows you a context message for the element under the cursor when emacs is idle. +#+BEGIN_SRC emacs-lisp :tangle org-ref.el +(defvar org-ref-message-timer nil + "Variable to store the link message timer in.") + + +(defun org-ref-show-link-messages () + "Turn on link messages. You will see a message in the +minibuffer when on a cite, ref or label link." + (interactive) + (or org-ref-message-timer + (setq org-ref-message-timer + (run-with-idle-timer 0.5 t 'org-ref-link-message)))) + + +(defun org-ref-cancel-link-messages () + "Stop showing messages in minibuffer when on a link." + (interactive) + (cancel-timer org-ref-message-timer) + (setq org-ref-message-timer nil)) + + +(when org-ref-show-citation-on-enter + (org-ref-show-link-messages)) + +;; this approach caused the selected region to not be highlighted any more. +; (add-hook 'post-command-hook 'org-ref-link-message)) +; (remove-hook 'post-command-hook 'org-ref-link-message)) +#+END_SRC + +** Messages for context under mouse pointer +Sometimes, when reading a document, I actually use the mouse more than the cursor. This code enables the mouse cursor to trigger a message in the minibuffer about what is under the cursor. I run this on a timer. + +The basic idea here is to get the mouse position, and if we can determine there is a character that (point) can move to, we move (point) and run the org-ref-link-message function. Since this runs on a timer, we store the last mouse position, and only run the function when the mouse has moved to avoid getting messages every time the timer runs. + +#+BEGIN_SRC emacs-lisp :tangle org-ref.el +(defvar org-ref-last-mouse-pos nil + "Stores last mouse position for use in `org-ref-mouse-message'.") + +(defun org-ref-can-move-p () + "See if a character is under the mouse. If so return the position for `goto-char'." + (let* ((line (cddr org-ref-last-mouse-pos)) + (col (cadr org-ref-last-mouse-pos))) + (save-excursion + (goto-char (window-start)) + (forward-line line) + (if + (> (- (line-end-position) (line-beginning-position)) col) + (progn (forward-char col) (point)) + nil)))) + + +(defun org-ref-mouse-message () + "Display message for link under mouse cursor" + (interactive) + (when (not (equal (mouse-position) org-ref-last-mouse-pos)) + (setq org-ref-last-mouse-pos (mouse-position)) + (let ((p (org-ref-can-move-p))) + (when p + (save-excursion + (goto-char p) + (org-ref-link-message)))))) + + +(defvar org-ref-message-timer-mouse nil + "Store mouse timer.") + + +(defvar org-ref-mouse-message-interval 0.5 + "How often to run the mouse message timer in seconds") + + +(defun org-ref-mouse-messages-on () + "Turn on mouse messages." + (interactive) + (or org-ref-message-timer-mouse + (setq org-ref-message-timer-mouse + (run-at-time "0.5 sec" + org-ref-mouse-message-interval + 'org-ref-mouse-message)))) + + +(defun org-ref-mouse-messages-off () + "Turn off mouse messages" + (interactive) + (cancel-timer org-ref-message-timer-mouse) + (setq org-ref-message-timer-mouse nil) + (message "Mouse messages are off")) +#+END_SRC + +#+RESULTS: +: org-ref-mouse-messages-off + * Links Most of this library is the creation of functional links to help with references and citations. ** General utilities @@ -471,7 +559,7 @@ This code provides some functions to generate a simple sorted bibliography in ht #+BEGIN_SRC emacs-lisp :tangle org-ref.el (defun org-ref-get-bibtex-keys () - "return a list of unique keys in the buffer." + "Return a list of unique keys in the buffer." (let ((keys '())) (org-element-map (org-element-parse-buffer) 'link (lambda (link) @@ -481,7 +569,9 @@ This code provides some functions to generate a simple sorted bibliography in ht (key (org-ref-split-and-strip-string (plist-get plist ':path))) (when (not (-contains? keys key)) - (setq keys (append keys (list key))))))))) + (setq keys (append keys (list key)))))))) + ;; set with-affiliated to get keys in captions + nil nil nil t) ;; Sort keys alphabetically (setq keys (cl-sort keys 'string-lessp :key 'downcase)) keys)) @@ -599,7 +689,6 @@ We use a link for the bibliography so that we can click on it to open the biblio (let* ((bibfile) ;; object is the link you clicked on (object (org-element-context)) - (link-string-beginning) (link-string-end)) @@ -913,26 +1002,37 @@ In long documents, a list of figures is not uncommon. Here we create a clickable #+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) - (+ (count-matches (format "label:%s\\b[^-:]" label) (point-min) (point-max) t) + "Counts number of matches for label in the document" + (+ (count-matches (format "label:%s\\b[^-:]" label) (point-min) (point-max)) ;; 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) + (count-matches (format "^#\\+tblname:\\s-*%s\\b[^-:]" label) (point-min) (point-max)) + (count-matches (format "\\label{%s}" label) (point-min) (point-max)) ;; 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)) + (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" (lambda (label) "on clicking count the number of label tags used in the buffer. A number greater than one means multiple labels!" - (message (format "%s occurences" (org-ref-count-labels label)))) + (let ((count (org-ref-count-labels label))) + (message (format "%s occurence%s" + count + (if (or (= count 0) + (> count 1)) + "s" + "")) + (org-ref-count-labels label)))) (lambda (keyword desc format) (cond ((eq format 'html) (format "()" path)) @@ -1040,7 +1140,7 @@ It would be nice to use completion to enter a ref link, where a list of labels i #+BEGIN_SRC emacs-lisp :tangle org-ref.el (defun org-ref-get-org-labels () - "find #+LABEL: labels" + "Return a list of #+LABEL: labels." (save-excursion (goto-char (point-min)) (let ((matches '())) @@ -1051,7 +1151,7 @@ matches))) #+BEGIN_SRC emacs-lisp :tangle org-ref.el (defun org-ref-get-custom-ids () - "return a list of custom_id properties in the buffer" + "Return a list of custom_id properties in the buffer." (let ((results '()) custom_id) (org-map-entries (lambda () @@ -1076,6 +1176,7 @@ Finally, we get the table names. #+BEGIN_SRC emacs-lisp :tangle org-ref.el (defun org-ref-get-tblnames () + "Return list of table names in the buffer." (org-element-map (org-element-parse-buffer 'element) 'table (lambda (table) (org-element-property :name table)))) @@ -1085,18 +1186,100 @@ Now, we can put all the labels together which will give us a list of candidates. #+BEGIN_SRC emacs-lisp :tangle org-ref.el (defun org-ref-get-labels () - "returns a list of labels in the buffer that you can make a ref link to. this is used to auto-complete ref links." + "Returns a list of labels in the buffer that you can make a ref link to. +This is used to auto-complete ref links and in helm menus." (save-excursion (save-restriction (widen) (goto-char (point-min)) (let ((matches '())) - (while (re-search-forward "label:\\([a-zA-z0-9:-]*\\)" (point-max) t) + ;; these are the label:stuff kinds + (while (re-search-forward "[^#+]label:\\([a-zA-z0-9:-]*\\)" (point-max) t) (add-to-list 'matches (match-string-no-properties 1) t)) - (append matches (org-ref-get-org-labels) (org-ref-get-latex-labels) (org-ref-get-tblnames) (org-ref-get-custom-ids)))))) + (append matches + (org-ref-get-org-labels) + (org-ref-get-latex-labels) + (org-ref-get-tblnames) + (org-ref-get-custom-ids)))))) #+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. +Let us make a helm function to insert a label link. This will help you enter unique labels by showing matching labels until they are all gone and you are left with a unique one. If you are on a link, it means you want to replace it. +#+BEGIN_SRC emacs-lisp :tangle org-ref.el +(defun org-ref-helm-insert-label-link () + "Insert a label link. helm just shows you what labels already exist. +If you are on a label link, replace it." + (interactive) + (let* ((labels (org-ref-get-labels)) + (cb (current-buffer))) + (helm :sources `(((name . "Existing labels") + (candidates . ,labels) + ;; default action is to open to the label + (action . (lambda (label) + ;; unfortunately I do not have markers here + (org-open-link-from-string (format "ref:%s" label)))) + ;; if you select a label, replace current one + (action . (lambda (label) + (switch-to-buffer ,cb) + (cond + ;; no prefix or on a link + ((equal helm-current-prefix-arg nil) + (let* ((object (org-element-context)) + (last-char (save-excursion + (goto-char (org-element-property :end object)) + (backward-char) + (if (looking-at " ") + " " + "")))) + (when (-contains? '("label") + (org-element-property :type object)) + ;; we are on a link, so replace it. + (setf + (buffer-substring + (org-element-property :begin object) + (org-element-property :end object)) + (concat + (replace-regexp-in-string + (org-element-property :path object) + label + (org-element-property :raw-link object)) + last-char))))) + ;; no prefix options defined + )))) + ;; no matching selection creates a new label + ((name . "Create new label") + (dummy) + ;; default action creates a new label, or replaces old one + (action . (lambda (label) + (switch-to-buffer ,cb) + (let* ((object (org-element-context)) + (last-char (save-excursion + (goto-char (org-element-property :end object)) + (backward-char) + (if (looking-at " ") + " " + "")))) + (if (-contains? '("label") + (org-element-property :type object)) + ;; we are on a link, so replace it. + (setf + (buffer-substring + (org-element-property :begin object) + (org-element-property :end object)) + (concat + (replace-regexp-in-string + (org-element-property :path object) + helm-pattern + (org-element-property :raw-link object)) + last-char)) + ;; new link + (insert + (concat + "label:" + (or label + helm-pattern)))))))))))) +#+END_SRC + +Now we create a 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 (defun org-ref-complete-link (&optional arg) @@ -1114,6 +1297,89 @@ Alternatively, you may want to just call a function that inserts a link with com (insert (org-ref-complete-link))) #+END_SRC +Another alternative ref insertion is to use helm. + +#+BEGIN_SRC emacs-lisp :tangle org-ref.el +(defun org-ref-helm-insert-ref-link () + "Helm menu to insert ref links to labels in the document. +If you are on link, replace with newly selected label. +Use C-u to insert a different kind of ref link. +Use C-u C-u to insert a [[#custom-id]] link +" + (interactive) + (let* ((labels (org-ref-get-labels)) + (bs (buffer-string)) + (contexts (with-temp-buffer + (insert bs) + (mapcar 'org-ref-get-label-context labels))) + (cb (current-buffer))) + + (helm :input (thing-at-point 'word) + :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))) + ;; default action to replace or insert ref link. + (action . (lambda (label) + (switch-to-buffer ,cb) + + (cond + ;; no prefix or on a link + ((equal helm-current-prefix-arg nil) + (let* ((object (org-element-context)) + (last-char (save-excursion + (goto-char (org-element-property :end object)) + (backward-char) + (if (looking-at " ") + " " + "")))) + (if (-contains? '("ref" "eqref" "pageref" "nameref") + (org-element-property :type object)) + ;; we are on a link, so replace it. + (setf + (buffer-substring + (org-element-property :begin object) + (org-element-property :end object)) + (concat + (replace-regexp-in-string + (org-element-property :path object) + label + (org-element-property :raw-link object)) + last-char)) + ;; insert a new link + (insert + (concat + "ref:" label)) + ))) + ;; one prefix, alternate ref link + ((equal helm-current-prefix-arg '(4)) + (insert + (concat + (helm :sources '((name . "Ref link types") + (candidates . ("ref" "eqref" "pageref" "nameref")) + (action . (lambda (x) x)))) + ":" label))) + ;; two prefixes, insert section custom-id link + ((equal helm-current-prefix-arg '(16)) + (insert + (format "[[#%s]]" label))) + )) + )))))) +#+END_SRC + +#+RESULTS: +: org-ref-helm-insert-ref-link + ** pageref This refers to the page of a label in LaTeX. @@ -1752,7 +2018,25 @@ We will want to generate formatting functions for each citation type. The reason ;; bibtex format (concat "\\" ,type (when desc (org-ref-format-citation-description desc)) "{" (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",") - "}")))))) + "}"))) + ;; for markdown we generate pandoc citations + ((eq format 'md) + (cond + (desc ;; pre and or post text + (let* ((text (split-string desc "::")) + (pre (car text)) + (post (cadr text))) + (concat + (format "[@%s," keyword) + (when pre (format " %s" pre)) + (when post (format ", %s" post)) + "]"))) + (t + (format "[%s]" + (mapconcat + (lambda (key) (concat "@" key)) + (org-ref-split-and-strip-string keyword) + "; ")))))))) #+END_SRC @@ -2046,7 +2330,6 @@ And at the end of the document put \makeglossaries. (format "\\Glspl{%s}" path))))) #+END_SRC - * Utilities ** create simple text citation from bibtex entry @@ -2262,8 +2545,8 @@ Here is the python script for uploading. *************** TODO document how to get the cookies *************** END - -#+BEGIN_SRC python :tangle upload_bibtex_citeulike.py +# :tangle upload_bibtex_citeulike.py +#+BEGIN_SRC python #!python import pickle, requests, sys @@ -2387,6 +2670,9 @@ If no bibliography is in the buffer the `reftex-default-bibliography' is used." #+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 @@ -2420,13 +2706,21 @@ Makes a new buffer with clickable links." (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 (-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)) - (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))))) - )))))) + (message-box "%s" link) + (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))))) + ))))) + ;; set with-affilates to t to get citations in a caption + nil nil nil t) (if bad-citations (progn @@ -2444,6 +2738,162 @@ Makes a new buffer with clickable links." (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))) + ))) + ;; add with-affiliates to get cites in caption + nil nil nil t) + (goto-char cp) + bad-citations)) + + +(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. @@ -2729,7 +3179,8 @@ To get a lighter weight message about the label, ref and cite links, we define a (point)) (progn (forward-line 4) - (point)))))))) + (point))))) + (throw 'result "!!! NO CONTEXT FOUND !!!")))) (defun org-ref-link-message () @@ -2746,12 +3197,18 @@ To get a lighter weight message about the label, ref and cite links, we define a ;; message some context about the label we are referring to ((string= type "ref") - (message (org-ref-get-label-context - (org-element-property :path object)))) + (message "%scount: %s" + (org-ref-get-label-context + (org-element-property :path object)) + (org-ref-count-labels + (org-element-property :path object)))) ((string= type "eqref") - (message (org-ref-get-label-context - (org-element-property :path object)))) + (message "%scount: %s" + (org-ref-get-label-context + (org-element-property :path object)) + (org-ref-count-labels + (org-element-property :path object)))) ;; message the count ((string= type "label") @@ -2763,7 +3220,53 @@ To get a lighter weight message about the label, ref and cite links, we define a " occurence" (when (or (= count 0) (> count 1)) - "s")))))))))) + "s"))))) + + ((string= type "custom-id") + (save-excursion + (org-open-link-from-string + (format "[[#%s]]" (org-element-property :path object))) + (message "%s" (org-get-heading)))) + + ;; 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))) + + ;; make sure we are in link and not before the : + (when (> link-string-beginning (point)) + (goto-char link-string-beginning)) + + ;; 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 + (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 + (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) + (message "!!! %s NOT FOUND !!!" bibfile)))) + ))))) #+END_SRC * Aliases @@ -2811,20 +3314,48 @@ 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. -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." - (let* ((object (org-element-context))) +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)) + (last-char (save-excursion + (goto-char (org-element-property :end object)) + (backward-char) + (if (looking-at " ") + " " + "")))) (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))) - ;;(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. + last-char)) + ;; and we want to go to the end of the new link + (goto-char + (org-element-property :end (org-element-context)))) + (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. @@ -2834,8 +3365,6 @@ Technically, this function should return a string that is inserted by helm. This (-contains? org-ref-cite-types (org-element-property :type (org-element-context))))) - ;;(message-box "at end of a link") - ;; (goto-char (org-element-property :end object)) (while (looking-back " ") (backward-char)) (insert (concat "," (mapconcat 'identity keys ",")))) @@ -2843,7 +3372,7 @@ Technically, this function should return a string that is inserted by helm. This (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)))) @@ -2856,18 +3385,34 @@ Technically, this function should return a string that is inserted by helm. This (setq helm-bibtex-format-citation-functions '((org-mode . helm-bibtex-format-org-ref))) -(defun org-ref-helm-insert-cite-link () - "org-ref function to use helm on the bibliography defined in the org-file." - (interactive) - (let ((helm-bibtex-bibliography (org-ref-find-bibliography))) - (helm-bibtex))) +(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. +With two prefix args, insert a label link." + (interactive "P") + (cond + ((equal arg nil) + (let ((helm-bibtex-bibliography (org-ref-find-bibliography))) + (helm-bibtex))) + ((equal arg '(4)) + (org-ref-helm-insert-ref-link)) + ((equal arg '(16)) + (org-ref-helm-insert-label-link)))) (require 'helm-bibtex) -(mapc (lambda (x) (add-to-list 'helm-bibtex-fallback-options x t)) - '(("Crossref" . "http://search.crossref.org/?q=%s") - ("Scopus" . "http://www.scopus.com/scopus/search/submit/xadvanced.url?searchfield=TITLE-ABS-KEY(%s)") - ("Open Web of Science" . (lambda () (browse-url "http://apps.webofknowledge.com"))))) +;; 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 '("WOS" . "http://gateway.webofknowledge.com/gateway/Gateway.cgi?topic=%s&GWVersion=2&SrcApp=WEB&SrcAuth=HSB&DestApp=UA&DestLinkType=GeneralSearchSummary") helm-bibtex-fallback-options)) #+END_SRC ** A helm click menu @@ -2879,11 +3424,13 @@ This code provides a helm interface to things you can do when you click on a cit (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))) + "!!! No entry found !!!" ))) (defun org-ref-cite-candidates () "Generate the list of possible candidates for click actions on a cite link.