X-Git-Url: https://git.donarmstrong.com/?p=org-ref.git;a=blobdiff_plain;f=org-ref.org;h=9665744c85bcf662ef33af3e9fa5de3cd738bb73;hp=06b89b38621cfd1fcb2f9ed17518a5350123a6b4;hb=181d000ee93496a7dca80cf64a28afba2b70e43c;hpb=37248aa86346505fbf10d36fbb872527936c91c7 diff --git a/org-ref.org b/org-ref.org index 06b89b3..9665744 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" @@ -371,6 +373,101 @@ The basic idea here is to get the mouse position, and if we can determine there #+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 @@ -1623,9 +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 @@ -1679,14 +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)))))))) @@ -2545,8 +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 @@ -3290,8 +3393,112 @@ 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) + "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." + (interactive "sKeywords: ") + (bibtex-set-field + "keywords" + (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") @@ -3302,11 +3509,12 @@ 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 @@ -3432,6 +3640,7 @@ 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." @@ -3565,6 +3774,42 @@ 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)