X-Git-Url: https://git.donarmstrong.com/?p=org-ref.git;a=blobdiff_plain;f=org-ref.org;h=f9bc3adb7f23e64267f0ff9902e57b3f0da6d258;hp=a4bd3ae11be1c98f8041d806f635b7f590b2107b;hb=39af3a30dbdc56a75ba17838cdd08d56ae2accf1;hpb=21e4c9b5f63623a9bcded19d7b1e3e0562cd4174 diff --git a/org-ref.org b/org-ref.org index a4bd3ae..f9bc3ad 100644 --- a/org-ref.org +++ b/org-ref.org @@ -1,3 +1,4 @@ +# -*- org-edit-src-content-indentation: 0; -*- #+TITLE: Org-ref - The best reference handling for org-mode #+AUTHOR: John Kitchin #+DATE: April 29, 2014 @@ -28,11 +29,16 @@ 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 +58,13 @@ 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 @@ -68,6 +76,7 @@ The only external require is reftex-cite (require 'helm) (require 'helm-config) (require 'helm-bibtex) +(require 'org) #+END_SRC ** Custom variables @@ -412,7 +421,7 @@ label:test (defcustom org-ref-label-color - "black" + "dark magenta" "Color of label links" :group 'org-ref) @@ -453,10 +462,16 @@ label:test "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: @@ -1617,7 +1632,6 @@ The first thing we need is to get the bibtex key we clicked on. point to get a comma, or the end of the link, and then backwards to get a comma, or the beginning of the link. that delimits the keyword we clicked on. We also strip the text properties." - (interactive) (let* ((object (org-element-context)) (link-string (org-element-property :path object))) ;; you may click on the part before the citations. here we make @@ -1671,7 +1685,6 @@ internal bibliographies falling back to what the user has set in org-ref-default-bibliography " - (interactive) (catch 'result (save-excursion (goto-char (point-min)) @@ -1731,7 +1744,6 @@ Finally, we want to know which file the key is in. #+BEGIN_SRC emacs-lisp :tangle org-ref.el (defun org-ref-get-bibtex-key-and-file (&optional key) "returns the bibtex key and file that it is in. If no key is provided, get one under point" - (interactive) (let ((org-ref-bibliography-files (org-ref-find-bibliography)) (file)) (unless key @@ -1776,14 +1788,14 @@ 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)))))))) @@ -1877,7 +1889,6 @@ Prompt for NEW-FILE includes bib files in org-ref-default-bibliography, and bib (defun org-ref-get-doi-at-point () "Get doi for key at point." - (interactive) (let* ((results (org-ref-get-bibtex-key-and-file)) (key (car results)) (bibfile (cdr results)) @@ -2142,15 +2153,18 @@ We create the links by mapping the function onto the list of defined link types. #+BEGIN_SRC emacs-lisp :tangle org-ref.el (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 ::." - (interactive) + "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]]." (cond ((string-match "::" desc) (format "[%s][%s]" (car (setq results (split-string desc "::"))) (cadr results))) (t (format "[%s]" desc)))) (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: ") @@ -2181,6 +2195,8 @@ 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. @@ -2224,8 +2240,7 @@ 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 @@ -2806,7 +2821,6 @@ 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 @@ -2935,6 +2949,7 @@ 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" @@ -3155,7 +3170,6 @@ 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 @@ -3165,7 +3179,7 @@ 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)) @@ -3187,12 +3201,13 @@ 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) + (defun org-ref-swap-citation-link (direction) "move citation at point in direction +1 is to the right, -1 to the left" (interactive) @@ -3212,7 +3227,17 @@ Sometimes it may be helpful to manually change the order of citations. These fun (org-ref-swap-keys i (- i 1) keys)) (setq keys (mapconcat 'identity keys ",")) ;; and replace the link with the sorted keys - (cl--set-buffer-substring begin end (concat type ":" keys " ")) + (cl--set-buffer-substring + begin end + (concat + type ":" keys + ;; It seems the space at the end can get consumed, so we see if there + ;; is a space, and add it if so. Sometimes there is a comma or period, + ;; then we do not want a space. + (when + (save-excursion + (goto-char end) + (looking-back " ")) " "))) ;; now go forward to key so we can move with the key (re-search-forward key) (goto-char (match-beginning 0))))) @@ -3387,8 +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))) + + +(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 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") @@ -3399,11 +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 @@ -3482,6 +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. @@ -3496,7 +3653,6 @@ With two prefix args, insert a label link." ((equal arg '(16)) (org-ref-helm-insert-label-link)))) -(require 'helm-bibtex) ;; add our own fallback entries where we want them. These appear in reverse order of adding in the menu (setq helm-bibtex-fallback-options @@ -3517,7 +3673,6 @@ 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))) @@ -3533,7 +3688,6 @@ This code provides a helm interface to things you can do when you click on a cit (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)) @@ -3638,8 +3792,10 @@ This is a list of cons cells '((\"description\" . action)). The action function '("Example" . (lambda () (message-box "You did it!"))) t) +;;;###autoload (defun org-ref-cite-click-helm (key) - "subtle points. + "Open helm for actions on a cite link. +subtle points. 1. get name and candidates before entering helm because we need the org-buffer. 2. switch back to the org buffer before evaluating the action. most of them need the point and buffer." (interactive) @@ -3667,44 +3823,43 @@ This is a list of cons cells '((\"description\" . action)). The action function 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 -(require 'hydra) -(setq hydra-is-helpful t) +(when (featurep 'hydra) + (require 'hydra) + (setq hydra-is-helpful t) -(defhydra org-ref-cite-hydra (:color blue) - " + (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)) + ("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 -#+RESULTS: -: org-ref-cite-hydra/body - -cite:oberhofer-2013-first * End of code #+BEGIN_SRC emacs-lisp :tangle org-ref.el (provide 'org-ref) + +;;; org-ref.el ends here #+END_SRC * Build :noexport: