X-Git-Url: https://git.donarmstrong.com/?p=org-ref.git;a=blobdiff_plain;f=org-ref.org;h=5df116f501d0e6b1bfdddd379fed40fd76cf0b3d;hp=148e98cd836f84634d4897f8eae631ef901454df;hb=8524cccb1fa0f9c1ebb5c1420abe5cbcff7f2e58;hpb=c6e740846a68ae8a2986459912c55ed2faa6574b diff --git a/org-ref.org b/org-ref.org index 148e98c..5df116f 100644 --- a/org-ref.org +++ b/org-ref.org @@ -28,11 +28,16 @@ With helm integration (default) you can: ** Header #+BEGIN_SRC emacs-lisp :tangle org-ref.el -;;; org-ref.el --- setup bibliography, cite, ref and label org-mode links. +;;; org-ref.el --- cite and cross-reference in org-mode ;; Copyright(C) 2014 John Kitchin ;; Author: John Kitchin +;; URL: https://github.com/jkitchin/org-ref +;; Version: 0.1 +;; Keywords: org-mode, cite, ref, label +;; Package-Requires: ((dash) (helm) (helm-bibtex)) + ;; This file is not currently part of GNU Emacs. ;; This program is free software; you can redistribute it and/or @@ -52,11 +57,13 @@ With helm integration (default) you can: ;;; Commentary: ;; -;; Lisp code to setup bibliography cite, ref and label org-mode links. also -;; sets up reftex and helm for org-mode citations. The links are clickable and -;; do things that are useful. You should really read org-ref.org for details. +;; Lisp code to setup bibliography cite, ref and label org-mode links. +;; also sets up reftex and helm for org-mode citations. The links are +;; clickable and do things that are useful. You should really read +;; org-ref.org for details. ;; -;; Package-Requires: ((dash) (helm) (helm-bibtex)) + +;;; Code: #+END_SRC ** requires @@ -66,7 +73,9 @@ The only external require is reftex-cite (require 'reftex-cite) (require 'dash) (require 'helm) +(require 'helm-config) (require 'helm-bibtex) +(require 'org) #+END_SRC ** Custom variables @@ -150,10 +159,11 @@ 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" @@ -390,7 +400,7 @@ ref:test label:test -#+BEGIN_SRC emacs-lisp +#+BEGIN_SRC emacs-lisp :tangle org-ref.el (defcustom org-ref-colorize-links t "When non-nil, change colors of links" @@ -410,7 +420,7 @@ label:test (defcustom org-ref-label-color - "black" + "dark magenta" "Color of label links" :group 'org-ref) @@ -420,7 +430,11 @@ label:test (setq org-ref-cite-re - (concat "\\(" (mapconcat 'identity org-ref-cite-types "\\|") "\\)" + (concat "\\(" (mapconcat + (lambda (x) + (replace-regexp-in-string "\*" "\\\\*" x) + ) + org-ref-cite-types "\\|") "\\)" ":\\([a-zA-Z0-9-_:]*,?\\)*")) @@ -434,20 +448,29 @@ label:test (defface org-ref-cite-face `((t (:inherit org-link :foreground ,org-ref-cite-color))) - "Color for cite links") + "Color for cite-like links in org-ref.") + (defface org-ref-label-face `((t (:inherit org-link :foreground ,org-ref-label-color))) - "Color for cite links") + "Color for ref links in org-ref.") + (defface org-ref-ref-face `((t (:inherit org-link :foreground ,org-ref-ref-color))) - "Color for cite links") + "Face for ref links in org-ref.") -(when org-ref-colorize-links + +(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: @@ -1705,9 +1728,15 @@ 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 @@ -1761,14 +1790,14 @@ 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)))))))) @@ -2126,16 +2155,22 @@ We will want to generate formatting functions for each citation type. The reason We create the links by mapping the function onto the list of defined link types. #+BEGIN_SRC emacs-lisp :tangle org-ref.el +;;;###autoload (defun org-ref-format-citation-description (desc) - "return formatted citation description. if the cite link has a description, it is optional text for the citation command. You can specify pre and post text by separating these with ::." + "Return formatted citation description. If the cite link has a +description, it is optional text for the citation command. You +can specify pre and post text by separating these with ::, for +example [[cite:key][pre text::post text]]." (interactive) (cond ((string-match "::" desc) (format "[%s][%s]" (car (setq results (split-string desc "::"))) (cadr results))) (t (format "[%s]" desc)))) +;;;###autoload (defun org-ref-define-citation-link (type &optional key) - "add a citation link for org-ref. With optional key, set the reftex binding. For example: + "Add a citation link of TYPE for org-ref. +With optional KEY, set the reftex binding. For example: (org-ref-define-citation-link \"citez\" ?z) will create a new citez link, with reftex key of z, and the completion function." (interactive "sCitation Type: \ncKey: ") @@ -2166,10 +2201,13 @@ and the completion function." (mapcar 'org-ref-define-citation-link org-ref-cite-types) #+END_SRC +#+RESULTS: + *** org-ref-insert-cite-link We need a convenient method to insert links. In reftex you use the keystroke C-c ], which gives you a minibuffer to search the bibtex files from. This function is bound to that same keystroke here [[*org-mode%20/%20reftex%20setup][org-mode / reftex setup]]. This function will append to a cite link if you call it while on a link. #+BEGIN_SRC emacs-lisp :tangle org-ref.el +;;;###autoload (defun org-ref-insert-cite-link (alternative-cite) "Insert a default citation link using reftex. If you are on a link, it appends to the end of the link, otherwise, a new link is @@ -2209,8 +2247,7 @@ inserted. Use a prefix arg to get a menu of citation types." (mapconcat 'identity (reftex-citation t) ","))))) ;; you pressed a C-u so we run this code - (reftex-citation))) - ) + (reftex-citation)))) #+END_SRC cite:zhou-2004-first-lda-u,paier-2006-errat,boes-2015-estim-bulk @@ -2235,6 +2272,7 @@ If you know the specific bibtex key, you may like to use completion directly. Yo Alternatively, you may shortcut the org-machinery with this command. You will be prompted for a citation type, and then offered key completion. #+BEGIN_SRC emacs-lisp :tangle org-ref.el +;;;###autoload (defun org-ref-insert-cite-with-completion (type) "Insert a cite link with completion" (interactive (list (ido-completing-read "Type: " org-ref-cite-types))) @@ -2245,6 +2283,7 @@ Alternatively, you may shortcut the org-machinery with this command. You will be org-mode already defines a store link function for bibtex entries. It does not store the link I want though, it only stores a brief citation of the entry. I want a citation link. Here is a function to do that. #+BEGIN_SRC emacs-lisp :tangle org-ref.el +;;;###autoload (defun org-ref-store-bibtex-entry-link () "Save a citation link to the current bibtex entry. Saves in the default link type." (interactive) @@ -2474,6 +2513,7 @@ This assumes you are in an article." ** open pdf from bibtex We bind this to a key here: [[*key%20bindings%20for%20utilities][key bindings for utilities]]. #+BEGIN_SRC emacs-lisp :tangle org-ref.el +;;;###autoload (defun org-ref-open-bibtex-pdf () "open pdf for a bibtex entry, if it exists. assumes point is in the entry of interest in the bibfile. but does not check that." @@ -2791,7 +2831,6 @@ Makes a new buffer with clickable links." (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)) - (message-box "%s" link) (setq bad-citations (append @@ -2920,6 +2959,7 @@ Here we develop a similar idea, but instead of an org-buffer with links, we crea 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 +;;;###autoload (defun org-ref () "Opens a helm interface to actions for org-ref. Shows bad citations, ref links and labels" @@ -3140,7 +3180,6 @@ I prefer citations in chronological order within a grouping. These functions sor #+BEGIN_SRC emacs-lisp :tangle org-ref.el (defun org-ref-get-citation-year (key) "get the year of an entry with key. Returns year as a string." - (interactive) (let* ((results (org-ref-get-bibtex-key-and-file key)) (bibfile (cdr results))) (with-temp-buffer @@ -3150,7 +3189,7 @@ I prefer citations in chronological order within a grouping. These functions sor )))) (defun org-ref-sort-citation-link () - "replace link at point with sorted link by year" + "Replace link at point with sorted link by year." (interactive) (let* ((object (org-element-context)) (type (org-element-property :type object)) @@ -3172,12 +3211,13 @@ I prefer citations in chronological order within a grouping. These functions sor Sometimes it may be helpful to manually change the order of citations. These functions define shift-arrow functions. #+BEGIN_SRC emacs-lisp :tangle org-ref.el (defun org-ref-swap-keys (i j keys) - "swap the keys in a list with index i and j" + "Swap the KEYS in a list with index I and J." (let ((tempi (nth i keys))) (setf (nth i keys) (nth j keys)) (setf (nth j keys) tempi)) keys) +;;;###autoload (defun org-ref-swap-citation-link (direction) "move citation at point in direction +1 is to the right, -1 to the left" (interactive) @@ -3264,7 +3304,7 @@ To get a lighter weight message about the label, ref and cite links, we define a (point))))) (throw 'result "!!! NO CONTEXT FOUND !!!")))) - +;;;###autoload (defun org-ref-link-message () "Print a minibuffer message about the link that point is on." (interactive) @@ -3372,8 +3412,138 @@ 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 :tangle org-ref.el +(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 :tangle org-ref.el +(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 :tangle org-ref.el +;; 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))) + +;;;###autoload +(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)) + +;;;###autoload +(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 helm-bibtex-show-entry (key) + "Show the entry in the BibTeX file. +The original function in helm-bibtex has a bug where it finds the +first key that partially matches. This version avoids that." + (catch 'break + (dolist (bibtex-file (if (listp helm-bibtex-bibliography) + helm-bibtex-bibliography + (list helm-bibtex-bibliography))) + (let ((buf (helm-bibtex-buffer-visiting bibtex-file)) + (entries '())) + (find-file bibtex-file) + (bibtex-map-entries + (lambda (key start end) + (add-to-list 'entries (cons key start)))) + (if (assoc key entries) + (progn + (goto-char (cdr (assoc key entries))) + (throw 'break t)) + (unless buf + (kill-buffer))))))) + +(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'." + (message "") + (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") @@ -3384,11 +3554,12 @@ 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 @@ -3467,6 +3638,7 @@ C-u C-u will change the key at point to the selected keys. (setq helm-bibtex-format-citation-functions '((org-mode . helm-bibtex-format-org-ref))) +;;;###autoload (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. @@ -3502,7 +3674,6 @@ This code provides a helm interface to things you can do when you click on a cit #+BEGIN_SRC emacs-lisp :tangle org-ref.el (defun org-ref-get-citation-string-at-point () "Get a string of a formatted citation" - (interactive) (let* ((results (org-ref-get-bibtex-key-and-file)) (key (car results)) (bibfile (cdr results))) @@ -3514,10 +3685,10 @@ 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." - (interactive) (let* ((results (org-ref-get-bibtex-key-and-file)) (key (car results)) (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key)) @@ -3621,7 +3792,7 @@ This is a list of cons cells '((\"description\" . action)). The action function 'org-ref-helm-user-candidates '("Example" . (lambda () (message-box "You did it!"))) t) - +;;;###autoload (defun org-ref-cite-click-helm (key) "subtle points. 1. get name and candidates before entering helm because we need the org-buffer. @@ -3647,9 +3818,47 @@ 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) + +;;; org-ref.el ends here #+END_SRC * Build :noexport: