X-Git-Url: https://git.donarmstrong.com/?p=org-ref.git;a=blobdiff_plain;f=org-ref.org;h=0cd567a69a30a6119015fbfd1b43acbecc031239;hp=b5429942f7665d8347131bc13164b0963d7cfe47;hb=b364e49eb183d660d9adb4267bc962b9e98183ae;hpb=c259c0584eafa5dfd5475ab1cb5007712b921e76 diff --git a/org-ref.org b/org-ref.org index b542994..0cd567a 100644 --- a/org-ref.org +++ b/org-ref.org @@ -66,6 +66,7 @@ The only external require is reftex-cite (require 'reftex-cite) (require 'dash) (require 'helm) +(require 'helm-config) (require 'helm-bibtex) #+END_SRC @@ -150,10 +151,11 @@ There are some variables needed later to tell this library where you store your (defcustom org-ref-cite-onclick-function 'org-ref-cite-click-helm - "Function that runs when you click on a cite link. The function must take no arguments. You may also use `org-ref-cite-onclick-minibuffer-menu' if you do not like helm." + "Function that runs when you click on a cite link. The function must take no arguments. You may also use `org-ref-cite-onclick-minibuffer-menu' if you do not like helm. If you like `hydra', consider using `org-ref-cite-hydra'." :type 'function :group 'org-ref) + (defcustom org-ref-show-citation-on-enter t "If non-nil add a hook function to show the citation summary in the minibuffer just by putting the cursor in a link" @@ -242,26 +244,6 @@ 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 @@ -297,6 +279,195 @@ 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 + "dark magenta" + "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.") + + +(defun org-ref-colorize-links () + "Colorize org-ref links." + (hi-lock-mode 1) + (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)) + + +(when org-ref-colorize-links + (add-hook 'org-mode-hook 'org-ref-colorize-links)) +#+END_SRC + +#+RESULTS: + + * Links Most of this library is the creation of functional links to help with references and citations. ** General utilities @@ -485,7 +656,7 @@ 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) @@ -495,7 +666,9 @@ 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)) @@ -1547,9 +1720,15 @@ Now, we can see if an entry is in a file. #+BEGIN_SRC emacs-lisp :tangle org-ref.el (defun org-ref-key-in-file-p (key filename) "determine if the key is in the file" - (interactive "skey: \nsFile: ") (save-current-buffer (let ((bibtex-files (list filename))) + ;; This is something I am trying because when the bibtex file is open, and + ;; you have added to it, the only way I find to get the update to update + ;; is to close it and reopen it. or to save it and revert it. + (when (get-file-buffer filename) + (set-buffer (get-file-buffer filename)) + (save-buffer) + (revert-buffer t t)) (bibtex-search-entry key t)))) #+END_SRC @@ -1603,14 +1782,14 @@ We need some convenience functions to open act on the citation at point. These w (catch 'done (let ((url (bibtex-autokey-get-field "url"))) (when url - (browse-url url) + (browse-url (s-trim 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))) + (browse-url (format "http://dx.doi.org/%s" (s-trim doi)))) (throw 'done nil)))))))) @@ -1942,7 +2121,25 @@ 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 @@ -2451,8 +2648,8 @@ 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 @@ -2612,13 +2809,21 @@ 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 @@ -2657,46 +2862,18 @@ 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)." @@ -3216,8 +3393,118 @@ I like convenience. Here are some aliases for faster typing. * Helm interface [[https://github.com/tmalsburg/helm-bibtex][helm-bibtex]] is a very cool interface to bibtex files. Out of the box though, it is not super convenient for org-ref. Here, we modify it to make it fit our workflow and extend it where needed. +Let us add keywords as a searchable field. +#+BEGIN_SRC emacs-lisp +(setq helm-bibtex-additional-search-fields '(keywords)) +#+END_SRC + +Next, we are going to add keywords to the helm interface. This modifies the helm-bibtex function to add our keywords. +#+BEGIN_SRC emacs-lisp +(defun helm-bibtex-candidates-formatter (candidates source) + "Formats BibTeX entries for display in results list." + (cl-loop + with width = (with-helm-window (window-width)) + for entry in candidates + for entry = (cdr entry) + for entry-key = (helm-bibtex-get-value entry 'entry-key) + for fields = (--map (helm-bibtex-clean-string + (helm-bibtex-get-value entry it " ")) + '(author title year has-pdf has-note entry-type)) + for fields = (-update-at 0 'helm-bibtex-shorten-authors fields) + for fields = (append fields + (list (or (helm-bibtex-get-value entry 'keywords) + "" ))) + collect + (cons (s-format "$0 $1 $2 $3 $4$5 $6" 'elt + (-zip-with (lambda (f w) (truncate-string-to-width f w 0 ?\s)) + fields (list 36 (- width 85) 4 1 1 7 7))) + entry-key))) + +#+END_SRC + +Next, we add some functions to add keywords to a bibtex entry using a helm interface, and a new action to add keywords to entries from helm-bibtex. +#+BEGIN_SRC emacs-lisp +;; adapted from bibtex-utils.el +;; these are candidates for selecting keywords/tags +(defun org-ref-bibtex-keywords () + "Get keywords defined in current bibtex file. +These are in the keywords field, and are comma or semicolon separated." + (save-excursion + (goto-char (point-min)) + (let (keywords kstring) + (while (re-search-forward "^\\s-*keywords.*{\\([^}]+\\)}" nil t) + ;; TWS - remove newlines/multiple spaces: + (setq kstring (replace-regexp-in-string "[ \t\n]+" " " (match-string 1))) + (mapc + (lambda (v) + (add-to-list 'keywords v t)) + (split-string kstring "\\(,\\|;\\)[ \n]*\\|{\\|}" t))) + keywords))) + + +(defun org-ref-set-bibtex-keywords (keywords &optional arg) + "Add KEYWORDS to a bibtex entry. +If KEYWORDS is a list, it is converted to a comma-separated string. The KEYWORDS are added to the beginning of the field. Otherwise KEYWORDS should be a string of comma-separate keywords." + (interactive "sKeywords: \nP") + (bibtex-set-field + "keywords" + (if arg + ;; replace with arg + (if (listp keywords) + (mapconcat 'identity keywords ", ") + keywords) + ;; else concatentate + (concat + (if (listp keywords) + (mapconcat 'identity keywords ", ") + keywords) + (when (not (string= "" (bibtex-autokey-get-field "keywords"))) + (concat ", " (bibtex-autokey-get-field "keywords")))))) + (save-buffer)) + + +(defun helm-tag-bibtex-entry () + "Helm interface to add keywords to a bibtex entry. +Run this with the point in a bibtex entry." + (interactive) + (let ((keyword-source `((name . "Existing keywords") + (candidates . ,(org-ref-bibtex-keywords)) + (action . (lambda (candidate) + (org-ref-set-bibtex-keywords + (mapconcat + 'identity + (helm-marked-candidates) + ", ")))))) + (fallback-source `((name . "Add new keywords") + (dummy) + (action . (lambda (candidate) + (org-ref-set-bibtex-keywords helm-pattern) + ))))) + (helm :sources '(keyword-source fallback-source)))) + + +(defun org-ref-helm-tag-entries (candidates) + "Set tags on selected bibtex entries from helm-bibtex. +User is prompted for tags. This function is called from `helm-bibtex'." + (let ((keywords (read-input "Keywords (comma separated): "))) + (loop for key in (helm-marked-candidates) + do + (save-window-excursion + (helm-bibtex-show-entry key) + (bibtex-set-field + "keywords" + (concat + keywords + ", " (bibtex-autokey-get-field "keywords"))) + (save-buffer))))) +#+END_SRC + +Next, adapt the helm-bibtex source with these features: + 1. Make the default action to insert selected keys. 2. Make open entry second action +3. Add some features for adding keywords to bibtex entries. + #+BEGIN_SRC emacs-lisp :tangle org-ref.el (setq helm-source-bibtex '((name . "BibTeX entries") @@ -3228,11 +3515,12 @@ I like convenience. Here are some aliases for faster typing. ("Show entry" . helm-bibtex-show-entry) ("Open PDF file (if present)" . helm-bibtex-open-pdf) ("Open URL or DOI in browser" . helm-bibtex-open-url-or-doi) - ("Insert reference" . helm-bibtex-insert-reference) + ("Insert formatted reference" . helm-bibtex-insert-reference) ("Insert BibTeX key" . helm-bibtex-insert-key) ("Insert BibTeX entry" . helm-bibtex-insert-bibtex) ("Attach PDF to email" . helm-bibtex-add-PDF-attachment) ("Edit notes" . helm-bibtex-edit-notes) + ("Add keywords to entries" . org-ref-helm-tag-entries) )))) #+END_SRC @@ -3279,8 +3567,7 @@ C-u C-u will change the key at point to the selected keys. last-char)) ;; and we want to go to the end of the new link (goto-char - (org-element-property :end (org-element-context))) - ) + (org-element-property :end (org-element-context)))) (t (message "Not found")))) @@ -3339,8 +3626,7 @@ 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 @@ -3360,6 +3646,7 @@ This code provides a helm interface to things you can do when you click on a cit (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. Checks for pdf and doi, and add appropriate functions." @@ -3493,6 +3780,42 @@ This is a list of cons cells '((\"description\" . action)). The action function #+RESULTS: : org-ref-cite-click-helm +** A hydra click interface +I like hydra a lot. Here we define a hydra menu you might like for the link click action. + +#+BEGIN_SRC emacs-lisp :tangle org-ref.el +(when (featurep 'hydra) + (require 'hydra) + (setq hydra-is-helpful t) + + (defhydra org-ref-cite-hydra (:color blue) + " +_p_: Open pdf _w_: WOS _g_: Google Scholar _K_: Copy citation to clipboard +_u_: Open url _r_: WOS related _P_: Pubmed _k_: Copy key to clipboard +_n_: Open notes _c_: WOS citing _C_: Crossref _f_: Copy bibtex entry to file +_o_: Open entry _e_: Email entry and pdf +" + ("o" org-ref-open-citation-at-point nil) + ("p" org-ref-open-pdf-at-point nil) + ("n" org-ref-open-notes-at-point nil) + ("u" org-ref-open-url-at-point nil) + ("w" org-ref-wos-at-point nil) + ("r" org-ref-wos-related-at-point nil) + ("c" org-ref-wos-citing-at-point nil) + ("g" org-ref-google-scholar-at-point nil) + ("P" org-ref-pubmed-at-point nil) + ("C" org-ref-crossref-at-point nil) + ("K" org-ref-copy-entry-as-summary nil) + ("k" (progn + (kill-new + (car (org-ref-get-bibtex-key-and-file)))) nil) + ("f" org-ref-copy-entry-at-point-to-file nil) + + ("e" (save-excursion + (org-ref-open-citation-at-point) + (email-bibtex-entry)) nil))) +#+END_SRC + * End of code #+BEGIN_SRC emacs-lisp :tangle org-ref.el (provide 'org-ref)