X-Git-Url: https://git.donarmstrong.com/?p=org-ref.git;a=blobdiff_plain;f=org-ref.org;h=79480c19a06704a503314c56d1e668f3ee502cc9;hp=dbaf75be246913a0f9625ea94c7573a77ec7fb69;hb=471e52526e14ad47b0c663fde5799c855703af34;hpb=3044d6641e83953951a3a576abde2cc7e51dc553 diff --git a/org-ref.org b/org-ref.org index dbaf75b..79480c1 100644 --- a/org-ref.org +++ b/org-ref.org @@ -12,6 +12,7 @@ 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: @@ -65,6 +66,7 @@ The only external require is reftex-cite (require 'reftex-cite) (require 'dash) (require 'helm) +(require 'helm-config) (require 'helm-bibtex) #+END_SRC @@ -241,26 +243,6 @@ 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 @@ -296,6 +278,189 @@ 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 + +** Color-coded links +Here we make the org-ref links a different color. + +citations are green +refs are blue +labels are black + +mailto:john + +cite:sokalski-2012-optim-ta,zhang-2011-spatial-tio2,li-2012-heter-ceram,li-2013-photoc + +cite*:sokalski-2012-optim-ta,zhang-2011-spatial-tio2,li-2012-heter-ceram,li-2013-photoc + +citenum:sokalski-2012-optim-ta,zhang-2011-spatial-tio2,li-2012-heter-ceram,li-2013-photoc + +ref:test + +label:test + +#+BEGIN_SRC emacs-lisp :tangle org-ref.el +(defcustom org-ref-colorize-links + t + "When non-nil, change colors of links" + :group 'org-ref) + + +(defcustom org-ref-cite-color + "forest green" + "Color of cite like links" + :group 'org-ref) + + +(defcustom org-ref-ref-color + "dark red" + "Color of ref like links" + :group 'org-ref) + + +(defcustom org-ref-label-color + "black" + "Color of label links" + :group 'org-ref) + + +(defvar org-ref-cite-re nil + "regexp for cite links") + + +(setq org-ref-cite-re + (concat "\\(" (mapconcat + (lambda (x) + (replace-regexp-in-string "\*" "\\\\*" x) + ) + org-ref-cite-types "\\|") "\\)" + ":\\([a-zA-Z0-9-_:]*,?\\)*")) + + +(setq org-ref-label-re + "label:\\([a-zA-Z0-9-_:]*,?\\)*") + + +(setq org-ref-ref-re + "ref:\\([a-zA-Z0-9-_:]*,?\\)*") + + +(defface org-ref-cite-face + `((t (:inherit org-link :foreground ,org-ref-cite-color))) + "Color for cite-like links in org-ref.") + + +(defface org-ref-label-face + `((t (:inherit org-link :foreground ,org-ref-label-color))) + "Color for ref links in org-ref.") + + +(defface org-ref-ref-face + `((t (:inherit org-link :foreground ,org-ref-ref-color))) + "Face for ref links in org-ref.") + + +(when org-ref-colorize-links + (highlight-regexp org-ref-cite-re 'org-ref-cite-face) + (highlight-regexp org-ref-label-re 'org-ref-label-face) + (highlight-regexp org-ref-ref-re 'org-ref-ref-face)) +#+END_SRC + +#+RESULTS: + + * Links Most of this library is the creation of functional links to help with references and citations. ** General utilities @@ -484,7 +649,7 @@ 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) @@ -494,7 +659,9 @@ 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)) @@ -934,7 +1101,7 @@ The label link provides a way to create labels in org-mode. We make it clickable ;; 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)) - (count-matches (format "\\label{%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)) (let ((custom-id-count 0)) @@ -1063,7 +1230,7 @@ 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 '())) @@ -1074,7 +1241,7 @@ 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 () @@ -1099,6 +1266,7 @@ 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)))) @@ -1108,18 +1276,24 @@ 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 -Let us make a helm function to insert a label link. This will help you enter unique labels. +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. @@ -1195,7 +1369,7 @@ If you are on a label link, replace it." 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. +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) @@ -1220,10 +1394,14 @@ Another alternative ref insertion is to use helm. "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)) - (contexts (mapcar 'org-ref-get-label-context 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) @@ -1281,7 +1459,12 @@ Use C-u to insert a different kind of ref link. (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: @@ -1925,7 +2108,25 @@ 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 @@ -2434,8 +2635,8 @@ 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 @@ -2595,13 +2796,21 @@ 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 @@ -2640,46 +2849,18 @@ Here we develop a similar idea, but instead of an org-buffer with links, we crea (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 (-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)) + (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)) -;; 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)." @@ -3089,7 +3270,6 @@ To get a lighter weight message about the label, ref and cite links, we define a (progn (forward-line 4) (point))))) - (beep) (throw 'result "!!! NO CONTEXT FOUND !!!")))) @@ -3107,19 +3287,24 @@ 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") (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" @@ -3170,7 +3355,6 @@ To get a lighter weight message about the label, ref and cite links, we define a (buffer-substring key-beginning key-end))) (if (file-exists-p bibfile) (message "%s exists." bibfile) - (beep) (message "!!! %s NOT FOUND !!!" bibfile)))) ))))) #+END_SRC @@ -3254,10 +3438,12 @@ C-u C-u will change the key at point to the selected keys. (replace-regexp-in-string (car (org-ref-get-bibtex-key-and-file)) ; key (mapconcat 'identity keys ",") ; new keys - (org-element-property :raw-link object) - ) + (org-element-property :raw-link object)) ;; replace space at end to avoid collapsing into next word. - last-char))) + 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")))) @@ -3316,8 +3502,7 @@ With two prefix args, insert a label link." 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)) + (-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 @@ -3335,7 +3520,6 @@ This code provides a helm interface to things you can do when you click on a cit (insert-file-contents bibfile) (bibtex-search-entry key) (org-ref-bib-citation))) - (beep) "!!! No entry found !!!" ))) (defun org-ref-cite-candidates ()