-#+TITLE: Org-ref - The best reference handling for org-mode
+#+TITLE: The org-ref manual
#+AUTHOR: John Kitchin
-#+DATE: April 29, 2014
-
-* Introduction
-
-This document is an experiment at creating a literate program to provide similar features as reftex for org-mode referencing. These features include:
-
-1. using completion to create links
-2. storing links to places,
-3. Clickable links that do useful things
-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:
-
-1. C-c ] to insert a citation link
- in helm-bibtex
- - Enter to insert or append citation(s)
- - C-u Enter to insert an alternative cite link
- - C-u C-u Enter to replace the citation at point
-2. C-u C-c ] to insert a ref link with helm completion
-3. C-u C-u C-c ] to insert a label with completion
-4. M-x org-ref to get a helm completion buffer with link checks, utilities and export options
-
-** Header
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-;;; org-ref.el --- setup bibliography, cite, ref and label org-mode links.
-
-;; Copyright(C) 2014 John Kitchin
-
-;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
-;; This file is not currently part of GNU Emacs.
-
-;; This program is free software; you can redistribute it and/or
-;; modify it under the terms of the GNU General Public License as
-;; published by the Free Software Foundation; either version 2, or (at
-;; your option) any later version.
-
-;; This program is distributed in the hope that it will be useful, but
-;; WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-;; General Public License for more details.
-
-;; You should have received a copy of the GNU General Public License
-;; along with this program ; see the file COPYING. If not, write to
-;; the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
-;; Boston, MA 02111-1307, USA.
-
-;;; 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.
-;;
-;; Package-Requires: ((dash) (helm) (helm-bibtex))
-#+END_SRC
-
-** requires
-The only external require is reftex-cite
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(require 'reftex-cite)
-(require 'dash)
-(require 'helm)
-(require 'helm-config)
-(require 'helm-bibtex)
-#+END_SRC
-
-** Custom variables
-There are some variables needed later to tell this library where you store your pdf files, where your notes file is, and your default bibliography. This variable is similar to the reftex-default-bibliography. I do not remember why I made it separate.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defgroup org-ref nil
- "customization group for org-ref")
-
-(defcustom org-ref-bibliography-notes
- nil
- "filename to where you will put all your notes about an entry in
- the default bibliography."
- :type 'file
- :group 'org-ref)
-
-(defcustom org-ref-default-bibliography
- nil
- "list of bibtex files to search for. You should use full-paths for each file."
- :type '(repeat :tag "List of bibtex files" file)
- :group 'org-ref)
-
-(defcustom org-ref-pdf-directory
- nil
- "directory where pdfs are stored by key. put a trailing / in"
- :type 'directory
- :group 'org-ref)
-
-(defcustom org-ref-default-citation-link
- "cite"
- "The default type of citation link to use"
- :type 'string
- :group 'org-ref)
-
-(defcustom org-ref-insert-cite-key
- "C-c ]"
- "Keyboard shortcut to insert a citation."
- :type 'string
- :group 'org-ref)
-
-(defcustom org-ref-bibliography-entry-format
- '(("article" . "%a, %t, <i>%j</i>, <b>%v(%n)</b>, %p (%y). <a href=\"%U\">link</a>. <a href=\"http://dx.doi.org/%D\">doi</a>.")
-
- ("book" . "%a, %t, %u (%y).")
-
- ("proceedings" . "%e, %t in %S, %u (%y).")
-
- ("inproceedings" . "%a, %t, %p, in %b, edited by %e, %u (%y)"))
-
- "string to format an entry. Just the reference, no numbering at the beginning, etc... see the `org-ref-reftex-format-citation' docstring for the escape codes."
- :type 'string
- :group 'org-ref)
-
-(defcustom org-ref-open-notes-function
- (lambda ()
- (org-show-entry)
- (show-branches)
- (show-children)
- (org-cycle '(64))
- ;;(org-tree-to-indirect-buffer)
- (outline-previous-visible-heading 1)
- (recenter-top-bottom 0))
- "User-defined way to open a notes entry. This is excecuted after the entry is found, with the cursor at the beginning of the headline. The default setting fully expands the notes, and moves the headline to the top of the buffer"
-:type 'function
-:group 'org-ref)
-
-
-(defcustom org-ref-open-pdf-function
- 'org-ref-open-pdf-at-point
-"User-defined function to open a pdf from a link. The function must get the key at point, and derive a path to the pdf file, then open it. The default function is `org-ref-open-pdf-at-point'."
- :type 'function
- :group 'org-ref)
-
-
-(defcustom org-ref-insert-cite-function
- 'org-ref-helm-insert-cite-link
- "Function to call to insert citation links. The default is `org-ref-helm-insert-cite-link' which uses `helm-bibtex'. org-ref modifies helm-bibtex a little bit to give org-mode citations, and to reorder default actions. You may use `org-ref-insert-cite-link' if you like the reftex interface."
- :type 'function
- :group 'org-ref)
-
-
-(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."
- :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"
- :group 'org-ref)
-
-#+END_SRC
-
-This next variable determines the citation types that are available in org-ref. Links for each one are automatically generated, and completion functions are automatically generated. Users may add to this list in their own init files.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defcustom org-ref-cite-types
- '("cite" "nocite" ;; the default latex cite commands
- ;; natbib cite commands, http://ctan.unixbrain.com/macros/latex/contrib/natbib/natnotes.pdf
- "citet" "citet*" "citep" "citep*"
- "citealt" "citealt*" "citealp" "citealp*"
- "citenum" "citetext"
- "citeauthor" "citeauthor*"
- "citeyear" "citeyear*"
- "Citet" "Citep" "Citealt" "Citealp" "Citeauthor"
- ;; biblatex commands
- ;; http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf
- "Cite"
- "parencite" "Parencite"
- "footcite" "footcitetext"
- "textcite" "Textcite"
- "smartcite" "Smartcite"
- "cite*" "parencite*" "supercite"
- "autocite" "Autocite" "autocite*" "Autocite*"
- "Citeauthor*"
- "citetitle" "citetitle*"
- "citedate" "citedate*"
- "citeurl"
- "fullcite" "footfullcite"
- ;; "volcite" "Volcite" cannot support the syntax
- "notecite" "Notecite"
- "pnotecite" "Pnotecite"
- "fnotecite"
- ;; multicites. Very limited support for these.
- "cites" "Cites" "parencites" "Parencites"
- "footcites" "footcitetexts"
- "smartcites" "Smartcites" "textcites" "Textcites"
- "supercites" "autocites" "Autocites"
- ;; for the bibentry package
- "bibentry"
- )
- "List of citation types known in org-ref"
- :type '(repeat :tag "List of citation types" string)
- :group 'org-ref)
-#+END_SRC
-
-We need a hook variable to store user-defined bibtex entry cleaning functions
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defcustom org-ref-clean-bibtex-entry-hook nil
- "Hook that is run in org-ref-clean-bibtex-entry. The functions should take no arguments, and operate on the bibtex entry at point."
- :group 'org-ref
- :type 'hook)
-#+END_SRC
-
-** Program variables
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defvar org-ref-bibliography-files
- nil
- "variable to hold bibliography files to be searched")
-#+END_SRC
-
-** org-mode / reftex setup
-
-We setup reftex here. We use a custom insert cite link function defined here: [[*org-ref-insert-cite-link][org-ref-insert-cite-link]]. We setup reftex to use our org citation format.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(require 'reftex)
-(defun org-mode-reftex-setup ()
- (and (buffer-file-name)
- (file-exists-p (buffer-file-name))
- (global-auto-revert-mode t)
- ;; I do not remember why I put this next line in. It doesn't
- ;; work for org-files. Nothing very bad happens, but it gives
- ;; an annoying error. Commenting it out for now.
- ;(reftex-parse-all
- )
- (make-local-variable 'reftex-cite-format)
- (setq reftex-cite-format 'org))
-
-;; define key for inserting citations
-(define-key org-mode-map
- (kbd org-ref-insert-cite-key)
- org-ref-insert-cite-function)
-
-(add-hook 'org-mode-hook 'org-mode-reftex-setup)
-
-(eval-after-load 'reftex-vars
- '(progn
- (add-to-list 'reftex-cite-format-builtin
- '(org "Org-mode citation"
- ((?\C-m . "cite:%l") ; default
- (?d . ",%l") ; for appending
- (?a . "autocite:%l")
- (?t . "citet:%l")
- (?T . "citet*:%l")
- (?p . "citep:%l")
- (?P . "citep*:%l")
- (?h . "citeauthor:%l")
- (?H . "citeauthor*:%l")
- (?y . "citeyear:%l")
- (?x . "citetext:%l")
- (?n . "nocite:%l")
- )))))
-#+END_SRC
-
-You may want to add new formats to the reftex-cite-format-builtin variable. Here is an example of adding two new formats. Note that this does not create the links.
-
-#+BEGIN_SRC emacs-lisp :tangle no
-;; add new format
-(setf (nth 2 (assoc 'org reftex-cite-format-builtin))
- (append (nth 2 (assoc 'org reftex-cite-format-builtin)) '((?W . "textcite:%l")
- (?z . "newcite:%l"))))
-#+END_SRC
-
-You can define a new citation link like this:
-#+BEGIN_SRC emacs-lisp :tangle no
-(org-ref-define-citation-link "citez" ?z)
-#+END_SRC
+#+DATE: 2015-03-15 Sun
+#+OPTIONS: toc:nil ^:{}
+#+LATEX_HEADER: \usepackage{natbib}
+\maketitle
+\tableofcontents
-** 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.")
+* Introduction to org-ref
+Org-ref is a library for org-mode cite:Dominik201408 that provides rich support for citations, labels and cross-references in org-mode. org-ref is especially suitable for org-mode documents destined for LaTeX export and scientific publication. org-ref is also extremely useful for research documents and notes. org-ref bundles several other libraries that provide functions to create and modify bibtex entries from a variety of sources, but most notably from a DOI.
+The basic idea of org-ref is that it defines a convenient interface to insert citations from a reference database (e.g. from a bibtex file(s)), and a set of functional org-mode links for citations, cross-references and labels that export properly to LaTeX, and that provide clickable functionality to the user. org-ref interfaces with helm-bibtex to facilitate citation entry, and it can also use reftex.
-(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))))
+org-ref provides a fairly large number of utilities for finding bad citations, extracting bibtex entries from citations in an org-file, and functions for interacting with bibtex entries. We find these utilities indispensable in scientific writing.
+org-ref is [[id:32B558A3-7B48-4581-982B-082017B0AEE8][customizable]].
-(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))
+org-ref has been in development since sometime in 2013. It was written to aid in the preparation of scientific manuscripts. We have published a lot of scientific articles with it so far cite:hallenbeck-2013-effec,mehta-2014-ident-poten,xu-2014-relat-elect,xu-2014-probin-cover,miller-2014-simul-temper,curnan-2014-effec-concen,boes-2015-estim-bulk,xu-2015-linear-respon,xu-2015-relat-between. Be sure to check out the supporting information files for each of these. The org source for the supporting information is usually embedded in the supporting information.
+There has been a lot of recent discussion on the org-mode mailing list about a citation syntax for org-mode. It is not clear what the impact of this on org-ref will be. The new syntax will more cleanly support pre/post text, and it will be separate from the links used in org-ref. It is not clear if the new syntax will support all of the citation types, especially those in biblatex, that are supported in org-ref. The new citations are likely to be clickable, and could share functionality with org-ref. The new citation syntax will not cover labels and cross-references though, so these links from org-ref will still exist. We anticipate a long life for org-ref.
-(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
+** Basic usage of org-ref
-** 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.
+*** Bibliography links
+index:bibliography index:bibliographystyle
-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.
+org-ref provides a bibliography link to specify which bibtex files to use in the document. You should use the filename with extension, and separate filenames by commas. This link is clickable; clicking on a filename will open the file. Also, if your cursor is on a filename, you will see a minibuffer message about whether the file exists or not. On export, the bibliography will appear at the position where the link is defined. Usually this link goes near the end of your document, e.g. like [[bibliography link][here]].
-#+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'.")
+There is also a nobibliography link, which is useful for specifying a bibliography file, but not listing a bibliography in the exported document.
-(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))))
+There is also a bibliographystyle link that specifies the style. This link does nothing but export to a LaTeX command.
+If you use biblatex, then you use an addbibresource link. biblatex support is not very well tested by me, because we do not use it.
-(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))))))
+*** Citations
+ :PROPERTIES:
+ :CUSTOM_ID: citations
+ :END:
+index:cite
+org-ref uses the [[bibliography link]] to determine which bibtex files to get citations from, and falls back to the bibtex files defined in the variable reftex-default-bibliography or org-ref-default-bibliography if no bibliography link is found.
-(defvar org-ref-message-timer-mouse nil
- "Store mouse timer.")
+For simple citation needs, org-ref is simple to use. At the point you want to insert a citation, you select the "Org -> org-ref -> Insert citation" menu (or use the key-binding C-c ] by default), select the reference(s) you want in the helm-bibtex buffer and press enter. The citation will be inserted automatically into your org-file. You "select" an entry by using the arrow keys to move up and down to the entry you want. You can narrow the selection by typing a pattern to match, e.g. author name, title words, year, keyword, etc... You can select multiple entries by pressing C-spc to mark enties in the helm-bibtex buffer.
+If the cursor is on a citation key, you should see a message in the minibuffer that summarizes which citation it refers to. If you click on a key, you should see a helm selection buffer with some actions to choose, including opening the bibtex entry, opening/getting a pdf for the entry, searching the entry in Web of Science, etc...
-(defvar org-ref-mouse-message-interval 0.5
- "How often to run the mouse message timer in seconds")
+The default citation type is [[id:32B558A3-7B48-4581-982B-082017B0AEE8][customizable]], and set to "cite". If you want another type of citation type, then type C-u before pressing enter in the helm-bibtex selection buffer. You will be prompted for the type of citation you actually want.
+Here is a list of supported citation types. You can customize this if you want. If you do not know what all these types are, you probably do not need them. The default cite is what you need. See http://ctan.unixbrain.com/macros/latex/contrib/natbib/natnotes.pdf
+ for the cite commands supported in bibtex index:natbib, and http://ctan.mirrorcatalogs.com/macros/latex/contrib/biblatex/doc/biblatex.pdf
+ for the commands supported in biblatex. For most scientific journals, only bibtex is supported. index:biblatex
-(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"))
+#+BEGIN_SRC emacs-lisp
+org-ref-cite-types
#+END_SRC
#+RESULTS:
-: org-ref-mouse-messages-off
+| cite | nocite | citet | citet* | citep | citep* | citealt | citealt* | citealp | citealp* | citenum | citetext | citeauthor | citeauthor* | citeyear | citeyear* | Citet | Citep | Citealt | Citealp | Citeauthor | Cite | parencite | Parencite | footcite | footcitetext | textcite | Textcite | smartcite | Smartcite | cite* | parencite* | supercite | autocite | Autocite | autocite* | Autocite* | Citeauthor* | citetitle | citetitle* | citedate | citedate* | citeurl | fullcite | footfullcite | notecite | Notecite | pnotecite | Pnotecite | fnotecite | cites | Cites | parencites | Parencites | footcites | footcitetexts | smartcites | Smartcites | textcites | Textcites | supercites | autocites | Autocites | bibentry |
-** Color-coded links
-Here we make the org-ref links a different color.
+If the cursor is on a citation, or at the end of the citation, and you add another citation, it will be appended to the current citation.
-citations are green
-refs are blue
-labels are black
+index:cite!replace
+If you want to /replace/ an existing key in a citation, put the cursor on the key, run the insert citation command, and type C-u C-u before pressing enter in the helm-bibtex selection buffer. The key will be replaced. Of course, you can just delete it yourself, and add a new key.
-mailto:john
+[[index:cite!shift]]
+Finally, if you do not like the order of the keys in a citation, you can put your cursor on a key and use shift-arrows (left or right) to move the key around. Alternatively, you can run the command org-ref-sort-citation-link which will sort the keys by year, oldest to newest.
-cite:sokalski-2012-optim-ta,zhang-2011-spatial-tio2,li-2012-heter-ceram,li-2013-photoc
+org-ref has basic support for pre/post text in citations. We have very little need for this in scientific publishing; we write pre text before the citation, and post text after it. However, you can get pre/post text by using a description in a cite link, with pre/post text separated by ::. For example, [[cite:Dominik201408][See page 20::, for example]]. It is a little awkward to see this because you cannot see the key. It is a low priority to find a fix for this, because it is not common in scientific publishing and you can always fall back to the old-fashioned LaTeX: \cite[See page 20][, for example]{Dominik201408}.
-cite*:sokalski-2012-optim-ta,zhang-2011-spatial-tio2,li-2012-heter-ceram,li-2013-photoc
+You may want to bind a hydra menu to a key-binding or key-chord. For example:
-citenum:sokalski-2012-optim-ta,zhang-2011-spatial-tio2,li-2012-heter-ceram,li-2013-photoc
+#+BEGIN_SRC emacs-lisp
+(key-chord-define-global "kk" 'org-ref-cite-hydra/body)
+#+END_SRC
-ref:test
+This will allow you to quickly press kk while on a cite link to access functions that can act on the link.
-label:test
+*** label links
+index:label
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defcustom org-ref-colorize-links
- t
- "When non-nil, change colors of links"
- :group 'org-ref)
+LaTeX uses labels to define places you can refer to. These can be labels in the captions of figures and tables, or labels in sections. We illustrate some uses here.
+label links are "functional" if you put your cursor on the link, you will get a message in the minibuffer showing you the number of occurrences of that label in the buffer. That number should be one! It is most preferable to put a label link into a caption like this.
+#+caption: Another simple table. label:tab-ydata
+| y |
+| 4 |
+| 5 |
-(defcustom org-ref-cite-color
- "forest green"
- "Color of cite like links"
- :group 'org-ref)
+org-ref can help you insert unique labels with the command elisp:org-ref-helm-insert-label-link. This will show you the existing labels, and insert your new label as a link. There is no default key-binding for this.
+*** ref links
+ :PROPERTIES:
+ :ID: 290260A1-F07C-4852-B4B3-CEE3E768AA3B
+ :END:
+index:ref
-(defcustom org-ref-ref-color
- "dark red"
- "Color of ref like links"
- :group 'org-ref)
+A ref link refers to a label of some sort. For example, you can refer to a table name, e.g. Table ref:table-1. You have to provide the context before the ref link, e.g. Table, Figure, Equation, Section, ....
+#+tblname: table-1
+#+caption: A simple table.
+| x |
+| 1 |
+| 2 |
-(defcustom org-ref-label-color
- "black"
- "Color of label links"
- :group 'org-ref)
+Or you can refer to an org-mode label as in Table ref:table-3.
+#+label: table-3
+#+caption: Another simple table.
+| y |
+|---|
+| 3 |
+| 2 |
-(defvar org-ref-cite-re nil
- "regexp for cite links")
+You can also refer to an org-ref label link as in Table ref:tab-ydata.
+To help you insert ref links, use the "Org->org-ref->Insert ref" menu, or run the command elisp:org-ref-helm-insert-ref-link. There is no default key-binding for this.
-(setq org-ref-cite-re
- (concat "\\(" (mapconcat
- (lambda (x)
- (replace-regexp-in-string "\*" "\\\\*" x)
- )
- org-ref-cite-types "\\|") "\\)"
- ":\\([a-zA-Z0-9-_:]*,?\\)*"))
+ref links are functional. If you put the cursor on a ref link, you will get a little message in the minibuffer with some context of the corresponding label. If you click on the ref link, the cursor will jump to the label.
+A brief note about references to a section. This only works if you put a label in the org-mode headline. Otherwise, you must use a CUSTOM_ID and a CUSTOM_ID link. For example section [[#citations]] has a CUSTOM_ID of citations. Section ref:sec-misc has a label link in the headline. That works, but is not too pretty.
-(setq org-ref-label-re
- "label:\\([a-zA-Z0-9-_:]*,?\\)*")
+**** Miscellaneous ref links label:sec-misc
+index:ref!pageref index:ref!nameref index:ref!eqref
+org-ref also provides these links:
-(setq org-ref-ref-re
- "ref:\\([a-zA-Z0-9-_:]*,?\\)*")
+- pageref :: The page a label is on
+- nameref :: The name of a section a label is in
+- eqref :: Puts the equation number in parentheses
+Note for eqref, you must use a LaTeX label like this:
-(defface org-ref-cite-face
- `((t (:inherit org-link :foreground ,org-ref-cite-color)))
- "Color for cite-like links in org-ref.")
+\begin{equation}
+e^x = 4 \label{eq:1}
+\end{equation}
+Then you can refer to Eq. eqref:eq:1 in your documents.
-(defface org-ref-label-face
- `((t (:inherit org-link :foreground ,org-ref-label-color)))
- "Color for ref links in org-ref.")
+*** Some other links
+[[index:list of tables]] [[index:list of figures]]
+org-ref provides clickable links for a list-of-tables:nil and list-of-figures:nil. We have to put some text in the link, anything will do. These export as listoftables and listoffigures LaTeX commands, and they are clickable links that open a mini table of contents with links to the tables and figures in the buffer. There are also interactive commands for this: elisp:org-ref-list-of-tables and elisp:org-ref-list-of-figures.
-(defface org-ref-ref-face
- `((t (:inherit org-link :foreground ,org-ref-ref-color)))
- "Face for ref links in org-ref.")
+** org-ref customization of helm-bibtex
+index:helm-bibtex
+org-ref adds a few new features to helm-bibtex. First, we add keywords as a searchable field. Second, org-ref modifies the helm-bibtex search buffer to include the keywords. Since keywords now can have a central role in searching, we add some functionality to add keywords from the helm-bibtex buffer as a new action.
-(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:
+We change the order of the actions in helm-bibtex to suit our work flow, and add some new actions. We define a format function for org-mode that is compatible with the usage defined in section [[#citations]]. Finally, we add some new fallback options for additional scientific search engines.
+** Some basic org-ref utilities
+[[index:bibtex!clean entry]]
-* Links
-Most of this library is the creation of functional links to help with references and citations.
-** General utilities
-We need several general utilities for this module. They are organized here. We frequently need to remove white space from the front and back of a string. Here we do that for a string.
+The command org-ref does a lot for you automatically. It will check the buffer for errors, e.g. multiply-defined labels, bad citations or ref links, and provide easy access to a few commands through a helm buffer.
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-strip-string (string)
- "strip leading and trailing whitespace from the string"
- (replace-regexp-in-string
- (concat search-whitespace-regexp "$" ) ""
- (replace-regexp-in-string
- (concat "^" search-whitespace-regexp ) "" string)))
-#+END_SRC
+org-ref-clean-bibtex-entry will sort the fields of a bibtex entry, clean it, and give it a bibtex key. This function does a lot of cleaning:
-It is helpful to make the previous function operate on a list of strings here.
+1. adds a comma if needed in the first line of the entry
+2. makes sure the doi field is an actual doi, and not a url.
+3. fixes bad year entries
+4. fixes empty pages
+5. Escapes & to \&
+6. generate a key according to your setup
+7. Runs your hook functions
+8. sorts the fields in the entry
+9. checks the buffer for non-ascii characters.
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-split-and-strip-string (string)
- "split key-string and strip keys. Assumes the key-string is comma delimited"
- (mapcar 'org-ref-strip-string (split-string string ",")))
-#+END_SRC
+This function has a hook org-ref-clean-bibtex-entry-hook, which you can add functions to of your own. Each function must work on a bibtex entry at point.
-** bibliography and bibliographystyle
-*** An html bibliography
-
-Reftex is no longer being developed. I want a url and doi option for formatting, so I am modifying this [[file:emacs-24.3/lisp/textmodes/reftex-cite.el::(defun%20reftex-format-citation%20(entry%20format)][function]] from reftex-cite to provide that. We need to modify the reftex-get-bib-field code a bit to remove enclosing braces and quotes so we can make nice looking links.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-reftex-get-bib-field (field entry &optional format)
- "similar to reftex-get-bib-field, but removes enclosing braces and quotes"
- (let ((result))
- (setq result (reftex-get-bib-field field entry format))
- (when (and (not (string= result "")) (string= "{" (substring result 0 1)))
- (setq result (substring result 1 -1)))
- (when (and (not (string= result "")) (string= "\"" (substring result 0 1)))
- (setq result (substring result 1 -1)))
- result))
-
-(defun org-ref-reftex-format-citation (entry format)
- "return a formatted string for the bibtex entry (from bibtex-parse-entry) according
-to the format argument. The format is a string with these percent escapes.
-
-In the format, the following percent escapes will be expanded.
-
-%l The BibTeX label of the citation.
-%a List of author names, see also `reftex-cite-punctuation'.
-%2a Like %a, but abbreviate more than 2 authors like Jones et al.
-%A First author name only.
-%e Works like %a, but on list of editor names. (%2e and %E work a well)
-
-It is also possible to access all other BibTeX database fields:
-%b booktitle %c chapter %d edition %h howpublished
-%i institution %j journal %k key %m month
-%n number %o organization %p pages %P first page
-%r address %s school %u publisher %t title
-%v volume %y year
-%B booktitle, abbreviated %T title, abbreviated
-%U url
-%D doi
-%S series
-
-Usually, only %l is needed. The other stuff is mainly for the echo area
-display, and for (setq reftex-comment-citations t).
-
-%< as a special operator kills punctuation and space around it after the
-string has been formatted.
-
-A pair of square brackets indicates an optional argument, and RefTeX
-will prompt for the values of these arguments.
-
-Beware that all this only works with BibTeX database files. When
-citations are made from the \bibitems in an explicit thebibliography
-environment, only %l is available."
- ;; Format a citation from the info in the BibTeX ENTRY
-
- (unless (stringp format) (setq format "\\cite{%l}"))
-
- (if (and reftex-comment-citations
- (string-match "%l" reftex-cite-comment-format))
- (error "reftex-cite-comment-format contains invalid %%l"))
-
- (while (string-match
- "\\(\\`\\|[^%]\\)\\(\\(%\\([0-9]*\\)\\([a-zA-Z]\\)\\)[.,;: ]*\\)"
- format)
- (let ((n (string-to-number (match-string 4 format)))
- (l (string-to-char (match-string 5 format)))
- rpl b e)
- (save-match-data
- (setq rpl
- (cond
- ((= l ?l) (concat
- (org-ref-reftex-get-bib-field "&key" entry)
- (if reftex-comment-citations
- reftex-cite-comment-format
- "")))
- ((= l ?a) (reftex-format-names
- (reftex-get-bib-names "author" entry)
- (or n 2)))
- ((= l ?A) (car (reftex-get-bib-names "author" entry)))
- ((= l ?b) (org-ref-reftex-get-bib-field "booktitle" entry "in: %s"))
- ((= l ?B) (reftex-abbreviate-title
- (org-ref-reftex-get-bib-field "booktitle" entry "in: %s")))
- ((= l ?c) (org-ref-reftex-get-bib-field "chapter" entry))
- ((= l ?d) (org-ref-reftex-get-bib-field "edition" entry))
- ((= l ?D) (org-ref-reftex-get-bib-field "doi" entry))
- ((= l ?e) (reftex-format-names
- (reftex-get-bib-names "editor" entry)
- (or n 2)))
- ((= l ?E) (car (reftex-get-bib-names "editor" entry)))
- ((= l ?h) (org-ref-reftex-get-bib-field "howpublished" entry))
- ((= l ?i) (org-ref-reftex-get-bib-field "institution" entry))
- ((= l ?j) (org-ref-reftex-get-bib-field "journal" entry))
- ((= l ?k) (org-ref-reftex-get-bib-field "key" entry))
- ((= l ?m) (org-ref-reftex-get-bib-field "month" entry))
- ((= l ?n) (org-ref-reftex-get-bib-field "number" entry))
- ((= l ?o) (org-ref-reftex-get-bib-field "organization" entry))
- ((= l ?p) (org-ref-reftex-get-bib-field "pages" entry))
- ((= l ?P) (car (split-string
- (org-ref-reftex-get-bib-field "pages" entry)
- "[- .]+")))
- ((= l ?s) (org-ref-reftex-get-bib-field "school" entry))
- ((= l ?S) (org-ref-reftex-get-bib-field "series" entry))
- ((= l ?u) (org-ref-reftex-get-bib-field "publisher" entry))
- ((= l ?U) (org-ref-reftex-get-bib-field "url" entry))
- ((= l ?r) (org-ref-reftex-get-bib-field "address" entry))
- ;; strip enclosing brackets from title if they are there
- ((= l ?t) (org-ref-reftex-get-bib-field "title" entry))
- ((= l ?T) (reftex-abbreviate-title
- (org-ref-reftex-get-bib-field "title" entry)))
- ((= l ?v) (org-ref-reftex-get-bib-field "volume" entry))
- ((= l ?y) (org-ref-reftex-get-bib-field "year" entry)))))
-
- (if (string= rpl "")
- (setq b (match-beginning 2) e (match-end 2))
- (setq b (match-beginning 3) e (match-end 3)))
- (setq format (concat (substring format 0 b) rpl (substring format e)))))
- (while (string-match "%%" format)
- (setq format (replace-match "%" t t format)))
- (while (string-match "[ ,.;:]*%<" format)
- (setq format (replace-match "" t t format)))
- ;; also replace carriage returns, tabs, and multiple whitespaces
- (setq format (replace-regexp-in-string "\n\\|\t\\|\s+" " " format))
- format)
-
-(defun org-ref-get-bibtex-entry-citation (key)
- "returns a string for the bibliography entry corresponding to key, and formatted according to the type in `org-ref-bibliography-entry-format'"
-
- (let ((org-ref-bibliography-files (org-ref-find-bibliography))
- (file) (entry) (bibtex-entry) (entry-type) (format))
-
- (setq file (catch 'result
- (loop for file in org-ref-bibliography-files do
- (if (org-ref-key-in-file-p key (file-truename file))
- (throw 'result file)
- (message "%s not found in %s" key (file-truename file))))))
-
- (with-temp-buffer
- (insert-file-contents file)
- (bibtex-search-entry key nil 0)
- (setq bibtex-entry (bibtex-parse-entry))
- (setq entry-type (downcase (cdr (assoc "=type=" bibtex-entry))))
- (setq format (cdr (assoc entry-type org-ref-bibliography-entry-format)))
- (if format
- (setq entry (org-ref-reftex-format-citation bibtex-entry format))
- (save-restriction
- (bibtex-narrow-to-entry)
- (setq entry (buffer-string)))))
- entry))
+#+BEGIN_SRC emacs-lisp
+(add-hook 'org-ref-clean-bibtex-entry-hook 'jmax-replace-nonascii)
#+END_SRC
#+RESULTS:
-: org-ref-reftex-format-citation
-
-Here is how to use the function. You call it with point in an entry in a bibtex file.
-
-#+BEGIN_SRC emacs-lisp :tangle no
-(let((org-ref-bibliography-entry-format "%a, %t, <i>%j</i>, <b>%v(%n)</b>, %p (%y). <a href=\"%U\">link</a>. <a href=\"http://dx.doi.org/%D\">doi</a>."))
- (org-ref-get-bibtex-entry-citation "armiento-2014-high"))
-#+END_SRC
-#+RESULTS:
-: Armiento, Kozinsky, Hautier, , Fornari \& Ceder, High-throughput screening of perovskite alloys for piezoelectric performance and thermodynamic stability, <i>Phys. Rev. B</i>, <b>89()</b>, 134103 (2014). <a href="http://link.aps.org/doi/10.1103/PhysRevB.89.134103">link</a>. <a href="http://dx.doi.org/10.1103/PhysRevB.89.134103">doi</a>.
-
-I am not sure why full author names are not used.
-
-This code provides some functions to generate a simple sorted bibliography in html. First we get all the keys in the buffer.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-get-bibtex-keys ()
- "Return a list of unique keys in the buffer."
- (let ((keys '()))
- (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 (not (-contains? keys 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))
-#+END_SRC
+| jmax-title-case-article | jmax-replace-nonascii |
-This function gets the html for one entry.
+org-ref-extract-bibtex-entries will create a bibtex file from the citations in the current buffer.
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-get-bibtex-entry-html (key)
- "returns an html string for the bibliography entry corresponding to key"
+** LaTeX export
+index:export!LaTeX
- (format "<li><a id=\"%s\">[%s] %s</a></li>" key key (org-ref-get-bibtex-entry-citation key)))
-#+END_SRC
+All org-ref links are designed to export to the corresponding LaTeX commands for citations, labels, refs and the bibliography/bibliography style. Once you have the LaTeX file, you have to build it, using the appropriate latex and bibtex commands. You can have org-mode do this for you with a setup like:
-Now, we map over the whole list of keys, and the whole bibliography, formatted as an unordered list.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-get-html-bibliography ()
- "Create an html bibliography when there are keys"
- (let ((keys (org-ref-get-bibtex-keys)))
- (when keys
- (concat "<h1>Bibliography</h1>
-<ul>"
- (mapconcat (lambda (x) (org-ref-get-bibtex-entry-html x)) keys "\n")
- "\n</ul>"))))
+#+BEGIN_SRC emacs-lisp
+(setq org-latex-pdf-process
+ '("pdflatex -interaction nonstopmode -output-directory %o %f"
+ "bibtex %b"
+ "pdflatex -interaction nonstopmode -output-directory %o %f"
+ "pdflatex -interaction nonstopmode -output-directory %o %f")
#+END_SRC
-I do not have plans to make a numbered bibliography with numbered citations anytime soon. This will require changing the way the citation links are exported, and keeping track of the numbers.
-
-*** An org bibliography
-You can export an org-file to an org-file or org-buffer (org-org-epxort-as-org). In this case, it would be useful convert the cite links to links to custom_ids, and the bibliography link to a first-level heading Bibliography with org-bibtex like headings for each entry. This code should enable this. Right now, it does not appear to work for org export though.
-
-First, we get the string for a single entry.
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-get-bibtex-entry-org (key)
- "returns an org string for the bibliography entry corresponding to key"
- (let ((org-ref-bibliography-files (org-ref-find-bibliography))
- (file) (entry) (bibtex-entry) (entry-type) (format))
-
- (setq file (catch 'result
- (loop for file in org-ref-bibliography-files do
- (if (org-ref-key-in-file-p key (file-truename file))
- (throw 'result file)
- (message "%s not found in %s" key (file-truename file))))))
-
- (with-temp-buffer
- (insert-file-contents file)
- (bibtex-search-entry key nil 0)
- (setq entry (bibtex-parse-entry))
- (format "** %s - %s
- :PROPERTIES:
- %s
- :END:
-" (org-ref-reftex-get-bib-field "author" entry)
-(org-ref-reftex-get-bib-field "title" entry)
-(concat " :CUSTOM_ID: " (org-ref-reftex-get-bib-field "=key=" entry) "\n"
- (mapconcat (lambda (element) (format " :%s: %s"
- (upcase (car element))
- (cdr element)))
- entry
- "\n"))))))
-#+END_SRC
-
-Now, we loop over the keys, and combine all the entries into a bibliography.
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-get-org-bibliography ()
- "Create an org bibliography when there are keys"
- (let ((keys (org-ref-get-bibtex-keys)))
- (when keys
- (concat "* Bibliography
-"
- (mapconcat (lambda (x) (org-ref-get-bibtex-entry-org x)) keys "\n")
- "\n"))))
-#+END_SRC
+** Other exports
+index:export!html index:export!ascii
+There is some basic support for HTML and ascii export. Not all bibtex entry types are supported, but basic support exists for articles and books. For a markdown export, the cite links are exported as Pandoc style links.
-*** An ascii bibliography
+* Other libraries in org-ref
+These are mostly functions for adding entries to bibtex files, modifying entries or for operating on bibtex files. Some new org-mode links are defined.
-This function gets the html for one entry.
+** doi-utils
+index:doi
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-get-bibtex-entry-ascii (key)
- "returns an ascii string for the bibliography entry corresponding to key"
-
- (format "[%s] %s" key (org-ref-get-bibtex-entry-citation key)))
-#+END_SRC
-
-Now, we map over the whole list of keys, and the whole bibliography, formatted as an unordered list.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-get-ascii-bibliography ()
- "Create an html bibliography when there are keys"
- (let ((keys (org-ref-get-bibtex-keys)))
- (when keys
- (concat
-"Bibliography
-=============
-"
- (mapconcat (lambda (x) (org-ref-get-bibtex-entry-ascii x)) keys "\n")
- "\n"))))
+This library adds two extremely useful tools for getting bibtex entries and pdf files of journal manuscripts. Add this to your emacs setup:
+#+BEGIN_SRC emacs-lisp
+(require 'doi-utils)
#+END_SRC
+The provides two important commands:
-*** the links
-We use a link for the bibliography so that we can click on it to open the bibliography file. The link may have more than one bibliography file in it, separated by commas. Clicking opens the file under the cursor. The bibliographies should be full filenames with the bib extension. Clicking on this link makes reftex-default-bibliography local and sets it to the list of files in the link. We need this to use reftex's searching capability.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(org-add-link-type "bibliography"
- ;; this code is run on clicking. The bibliography
- ;; may contain multiple files. this code finds the
- ;; one you clicked on and opens it.
- (lambda (link-string)
- ;; get link-string boundaries
- ;; we have to go to the beginning of the line, and then search forward
-
- (let* ((bibfile)
- ;; object is the link you clicked on
- (object (org-element-context))
- (link-string-beginning)
- (link-string-end))
-
- (save-excursion
- (goto-char (org-element-property :begin object))
- (search-forward link-string nil nil 1)
- (setq link-string-beginning (match-beginning 0))
- (setq link-string-end (match-end 0)))
-
- ;; We set the reftex-default-bibliography
- ;; here. it should be a local variable only in
- ;; the current buffer. We need this for using
- ;; reftex to do citations.
- (set (make-local-variable 'reftex-default-bibliography)
- (split-string (org-element-property :path object) ","))
-
- ;; now if we have comma separated bibliographies
- ;; we find the one clicked on. we want to
- ;; search forward to next comma from point
- (save-excursion
- (if (search-forward "," link-string-end 1 1)
- (setq key-end (- (match-end 0) 1)) ; we found a match
- (setq key-end (point)))) ; no comma found so take the point
- ;; and backward to previous comma from point
- (save-excursion
- (if (search-backward "," link-string-beginning 1 1)
- (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
- (setq key-beginning (point)))) ; no match found
- ;; save the key we clicked on.
- (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
- (find-file bibfile))) ; open file on click
-
- ;; formatting code
- (lambda (keyword desc format)
- (cond
- ((eq format 'org) (org-ref-get-org-bibliography))
- ((eq format 'ascii) (org-ref-get-ascii-bibliography))
- ((eq format 'html) (org-ref-get-html-bibliography))
- ((eq format 'latex)
- ;; write out the latex bibliography command
- (format "\\bibliography{%s}" (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
- (mapcar 'expand-file-name
- (split-string keyword ","))
- ",")))))))
-
-#+END_SRC
-
-Believe it or not, sometimes it makes sense /not/ to include the bibliography in a document (e.g. when you are required to submit references as a separate file). To generate the references, in another file, you must make a little tex file with these contents, and then compile it.
-
-#+BEGIN_LaTeX
- \input{project-description.bbl}
-#+END_LaTeX
-
-Here, we make a =nobibliography= link that acts like the bibliography, enables creation of the bbl file, but does not put an actual bibliography in the file.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(org-add-link-type "nobibliography"
- ;; this code is run on clicking. The bibliography
- ;; may contain multiple files. this code finds the
- ;; one you clicked on and opens it.
- (lambda (link-string)
- ;; get link-string boundaries
- ;; we have to go to the beginning of the line, and then search forward
-
- (let* ((bibfile)
- ;; object is the link you clicked on
- (object (org-element-context))
-
- (link-string-beginning)
- (link-string-end))
-
- (save-excursion
- (goto-char (org-element-property :begin object))
- (search-forward link-string nil nil 1)
- (setq link-string-beginning (match-beginning 0))
- (setq link-string-end (match-end 0)))
-
- ;; We set the reftex-default-bibliography
- ;; here. it should be a local variable only in
- ;; the current buffer. We need this for using
- ;; reftex to do citations.
- (set (make-local-variable 'reftex-default-bibliography)
- (split-string (org-element-property :path object) ","))
-
- ;; now if we have comma separated bibliographies
- ;; we find the one clicked on. we want to
- ;; search forward to next comma from point
- (save-excursion
- (if (search-forward "," link-string-end 1 1)
- (setq key-end (- (match-end 0) 1)) ; we found a match
- (setq key-end (point)))) ; no comma found so take the point
- ;; and backward to previous comma from point
- (save-excursion
- (if (search-backward "," link-string-beginning 1 1)
- (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
- (setq key-beginning (point)))) ; no match found
- ;; save the key we clicked on.
- (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
- (find-file bibfile))) ; open file on click
-
- ;; formatting code
- (lambda (keyword desc format)
- (cond
- ((eq format 'org) (org-ref-get-org-bibliography))
- ((eq format 'ascii) (org-ref-get-ascii-bibliography))
- ((eq format 'html) (org-ref-get-html-bibliography))
- ((eq format 'latex)
- ;; write out the latex bibliography command
-
-; (format "{\\setbox0\\vbox{\\bibliography{%s}}}"
-; (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
-; (mapcar 'expand-file-name
-; (split-string keyword ","))
-; ",")))
-
- (format "\\nobibliography{%s}"
- (replace-regexp-in-string "\\.bib" "" (mapconcat 'identity
- (mapcar 'expand-file-name
- (split-string keyword ","))
- ",")))
-
- ))))
-#+END_SRC
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(org-add-link-type "printbibliography"
- (lambda (arg) (message "Nothing implemented for clicking here."))
- (lambda (keyword desc format)
- (cond
- ((eq format 'org) (org-ref-get-org-bibliography))
- ((eq format 'html) (org-ref-get-html-bibliography))
- ((eq format 'latex)
- ;; write out the biblatex bibliography command
- "\\printbibliography"))
-))
-#+END_SRC
-
-We also create a bibliographystyle link. There is nothing to do on clicking here, and we create it for consistency. This sets the style for latex export, so use something appropriate there, e.g. unsrt, plain, plainnat, ...
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(org-add-link-type "bibliographystyle"
- (lambda (arg) (message "Nothing implemented for clicking here."))
- (lambda (keyword desc format)
- (cond
- ((eq format 'latex)
- ;; write out the latex bibliography command
- (format "\\bibliographystyle{%s}" keyword)))))
-#+END_SRC
+- doi-utils-add-bibtex-entry-from-doi
+This will prompt you for a DOI, and a bibtex file, and then try to get the bibtex entry, and pdf of the article.
-*** Completion for bibliography link
-It would be nice
+- doi-utils-add-entry-from-crossref-query
+This will prompt you for a query string, which is usually the title of an article, or a free-form text citation of an article. Then you will get a helm buffer of matching items, which you can choose from to insert a new bibtex entry into a bibtex file.
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-bibliography-complete-link (&optional arg)
- (format "bibliography:%s" (read-file-name "enter file: " nil nil t)))
+This library also redefines the org-mode doi link. Now, when you click on this link you will get a menu of options, e.g. to open a bibtex entry or a pdf if you have it, or to search the doi in some scientific search engines. Try it out doi:10.1021/jp511426q.
-(defun org-ref-insert-bibliography-link ()
- "insert a bibliography with completion"
- (interactive)
- (insert (org-bibliography-complete-link)))
-#+END_SRC
+** jmax-bibtex
+These are functions I use often in bibtex files.
-** addbibresource
-This is apparently used for biblatex.
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(org-add-link-type "addbibresource"
- ;; this code is run on clicking. The addbibresource
- ;; may contain multiple files. this code finds the
- ;; one you clicked on and opens it.
- (lambda (link-string)
- ;; get link-string boundaries
- ;; we have to go to the beginning of the line, and then search forward
-
- (let* ((bibfile)
- ;; object is the link you clicked on
- (object (org-element-context))
-
- (link-string-beginning)
- (link-string-end))
-
- (save-excursion
- (goto-char (org-element-property :begin object))
- (search-forward link-string nil nil 1)
- (setq link-string-beginning (match-beginning 0))
- (setq link-string-end (match-end 0)))
-
- ;; We set the reftex-default-addbibresource
- ;; here. it should be a local variable only in
- ;; the current buffer. We need this for using
- ;; reftex to do citations.
- (set (make-local-variable 'reftex-default-addbibresource)
- (split-string (org-element-property :path object) ","))
-
- ;; now if we have comma separated bibliographies
- ;; we find the one clicked on. we want to
- ;; search forward to next comma from point
- (save-excursion
- (if (search-forward "," link-string-end 1 1)
- (setq key-end (- (match-end 0) 1)) ; we found a match
- (setq key-end (point)))) ; no comma found so take the point
- ;; and backward to previous comma from point
- (save-excursion
- (if (search-backward "," link-string-beginning 1 1)
- (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
- (setq key-beginning (point)))) ; no match found
- ;; save the key we clicked on.
- (setq bibfile (org-ref-strip-string (buffer-substring key-beginning key-end)))
- (find-file bibfile))) ; open file on click
-
- ;; formatting code
- (lambda (keyword desc format)
- (cond
- ((eq format 'html) (format "")); no output for html
- ((eq format 'latex)
- ;; write out the latex addbibresource command
- (format "\\addbibresource{%s}" keyword)))))
-#+END_SRC
+*** Generate new bibtex files with adapted journal names
+The variable jmax-bibtex-journal-abbreviations contains a mapping of a short string to a full journal title, and an abbreviated journal title. We can use these to create new versions of a bibtex file with full or abbreviated journal titles. You can add new strings like this:
-** List of Figures
-
-In long documents, a list of figures is not uncommon. Here we create a clickable link that generates a temporary buffer containing a list of figures in the document, and their captions. We make a function that can be called interactively, and define a link type that is rendered in LaTeX to create the list of figures.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-list-of-figures (&optional arg)
- "Generate buffer with list of figures in them"
- (interactive)
- (save-excursion (widen)
- (let* ((c-b (buffer-name))
- (counter 0)
- (list-of-figures
- (org-element-map (org-element-parse-buffer) 'link
- (lambda (link)
- "create a link for to the figure"
- (when
- (and (string= (org-element-property :type link) "file")
- (string-match-p
- "[^.]*\\.\\(png\\|jpg\\|eps\\|pdf\\)$"
- (org-element-property :path link)))
- (incf counter)
-
- (let* ((start (org-element-property :begin link))
- (parent (car (cdr (org-element-property :parent link))))
- (caption (caaar (plist-get parent :caption)))
- (name (plist-get parent :name)))
- (if caption
- (format
- "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]] %s\n"
- c-b start counter (or name "") caption)
- (format
- "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][figure %s: %s]]\n"
- c-b start counter (or name "")))))))))
- (switch-to-buffer "*List of Figures*")
- (setq buffer-read-only nil)
- (org-mode)
- (erase-buffer)
- (insert (mapconcat 'identity list-of-figures ""))
- (setq buffer-read-only t)
- (use-local-map (copy-keymap org-mode-map))
- (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
-
-(org-add-link-type
- "list-of-figures"
- 'org-ref-list-of-figures ; on click
- (lambda (keyword desc format)
- (cond
- ((eq format 'latex)
- (format "\\listoffigures")))))
+#+BEGIN_SRC emacs-lisp
+(add-to-list 'jmax-bibtex-journal-abbreviations
+ '("JIR" "Journal of Irreproducible Research" "J. Irrep. Res."))
#+END_SRC
-** List of Tables
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-list-of-tables (&optional arg)
- "Generate a buffer with a list of tables"
- (interactive)
- (save-excursion
- (widen)
- (let* ((c-b (buffer-name))
- (counter 0)
- (list-of-tables
- (org-element-map (org-element-parse-buffer 'element) 'table
- (lambda (table)
- "create a link for to the table"
- (incf counter)
- (let ((start (org-element-property :begin table))
- (name (org-element-property :name table))
- (caption (caaar (org-element-property :caption table))))
- (if caption
- (format
- "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]] %s\n"
- c-b start counter (or name "") caption)
- (format
- "[[elisp:(progn (switch-to-buffer \"%s\")(widen)(goto-char %s))][table %s: %s]]\n"
- c-b start counter (or name ""))))))))
- (switch-to-buffer "*List of Tables*")
- (setq buffer-read-only nil)
- (org-mode)
- (erase-buffer)
- (insert (mapconcat 'identity list-of-tables ""))
- (setq buffer-read-only t)
- (use-local-map (copy-keymap org-mode-map))
- (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))))
-
-(org-add-link-type
- "list-of-tables"
- 'org-ref-list-of-tables
- (lambda (keyword desc format)
- (cond
- ((eq format 'latex)
- (format "\\listoftables")))))
-#+END_SRC
-** label
-
-The label link provides a way to create labels in org-mode. We make it clickable because we want to make sure labels are unique. This code will tell you how many instances of a label are found. We search for label links, LaTeX labels, and org-mode format for labels, tblnames too.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-count-labels (label)
- "Counts number of matches for label in the document"
- (+ (count-matches (format "label:%s\\b[^-:]" label) (point-min) (point-max))
- ;; 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}" 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))
- (org-map-entries
- (lambda ()
- (when (string= label (org-entry-get (point) "CUSTOM_ID"))
- (setq custom-id-count (+ 1 custom-id-count)))))
- custom-id-count)))
-
-(org-add-link-type
- "label"
- (lambda (label)
- "on clicking count the number of label tags used in the buffer. A number greater than one means multiple labels!"
- (let ((count (org-ref-count-labels label)))
- (message (format "%s occurence%s"
- count
- (if (or (= count 0)
- (> count 1))
- "s"
- ""))
- (org-ref-count-labels label))))
- (lambda (keyword desc format)
- (cond
- ((eq format 'html) (format "(<label>%s</label>)" path))
- ((eq format 'latex)
- (format "\\label{%s}" keyword)))))
-#+END_SRC
+- jmax-bibtex-generate-longtitles :: Generate a bib file with long titles as
+ defined in `jmax-bibtex-journal-abbreviations'
+- jmax-bibtex-generate-shorttitles :: Generate a bib file with short titles as
+ defined in `jmax-bibtex-journal-abbreviations'
-We want to store links on labels, so you can put the cursor on the label, press C-c l, and later use C-c C-l to insert a link to the label. We also want to store links to tables with a table name, and for sections with CUSTOM_ID.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-label-store-link ()
- "store a link to a label. The output will be a ref to that label"
- ;; First we have to make sure we are on a label link.
- (let* ((object (org-element-context)))
- (when (and (equal (org-element-type object) 'link)
- (equal (org-element-property :type object) "label"))
- (org-store-link-props
- :type "ref"
- :link (concat "ref:" (org-element-property :path object))))
-
- ;; Store link on table
- (when (equal (org-element-type object) 'table)
- (org-store-link-props
- :type "ref"
- :link (concat "ref:" (org-element-property :name object))))
-
-;; it turns out this does not work. you can already store a link to a heading with a CUSTOM_ID
- ;; store link on heading with custom_id
-; (when (and (equal (org-element-type object) 'headline)
-; (org-entry-get (point) "CUSTOM_ID"))
-; (org-store-link-props
-; :type "ref"
-; :link (concat "ref:" (org-entry-get (point) "CUSTOM_ID"))))
-
- ;; and to #+label: lines
- (when (and (equal (org-element-type object) 'paragraph)
- (org-element-property :name object))
- (org-store-link-props
- :type "ref"
- :link (concat "ref:" (org-element-property :name object))))
-))
-
-(add-hook 'org-store-link-functions 'org-label-store-link)
-#+END_SRC
-** ref
-
-The ref link allows you make links to labels. Clicking on the link takes you to the label, and provides a mark to go back to.
-
-At the moment, ref links are not usable for section links. You need [[#CUSTOM_ID]] type links.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(org-add-link-type
- "ref"
- (lambda (label)
- "on clicking goto the label. Navigate back with C-c &"
- (org-mark-ring-push)
- ;; next search from beginning of the buffer
-
- ;; it is possible you would not find the label if narrowing is in effect
- (widen)
-
- (unless
- (or
- ;; our label links
- (progn
- (goto-char (point-min))
- (re-search-forward (format "label:%s\\b" label) nil t))
-
- ;; a latex label
- (progn
- (goto-char (point-min))
- (re-search-forward (format "\\label{%s}" label) nil t))
-
- ;; #+label: name org-definition
- (progn
- (goto-char (point-min))
- (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
-
- ;; org tblname
- (progn
- (goto-char (point-min))
- (re-search-forward (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t))
-
-;; Commented out because these ref links do not actually translate correctly in LaTeX.
-;; you need [[#label]] links.
- ;; CUSTOM_ID
-; (progn
-; (goto-char (point-min))
-; (re-search-forward (format ":CUSTOM_ID:\s-*\\(%s\\)" label) nil t))
- )
- ;; we did not find anything, so go back to where we came
- (org-mark-ring-goto)
- (error "%s not found" label))
- (org-show-entry)
- (message "go back with (org-mark-ring-goto) `C-c &`"))
- ;formatting
- (lambda (keyword desc format)
- (cond
- ((eq format 'html) (format "(<ref>%s</ref>)" path))
- ((eq format 'latex)
- (format "\\ref{%s}" keyword)))))
-#+END_SRC
+*** Modifying bibtex entries
-It would be nice to use completion to enter a ref link, where a list of labels is provided. The following code searches the buffer for org and latex labels, custom_ids, and table names as potential items to make a ref link to.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-get-org-labels ()
- "Return a list of #+LABEL: labels."
- (save-excursion
- (goto-char (point-min))
- (let ((matches '()))
- (while (re-search-forward "^#\\+label:\\s-+\\(.*\\)\\b" (point-max) t)
- (add-to-list 'matches (match-string-no-properties 1) t))
-matches)))
-#+END_SRC
+- jmax-stringify-journal-name :: replace a journal name with a string in
+ `jmax-bibtex-journal-abbreviations'
+- jmax-set-journal-string :: in a bibtex entry run this to replace the journal
+ with a string selected interactively.
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-get-custom-ids ()
- "Return a list of custom_id properties in the buffer."
- (let ((results '()) custom_id)
- (org-map-entries
- (lambda ()
- (let ((custom_id (org-entry-get (point) "CUSTOM_ID")))
- (when (not (null custom_id))
- (setq results (append results (list custom_id)))))))
-results))
-#+END_SRC
+- jmax-title-case-article :: title case the title in an article entry.
+- jmax-sentence-case-article :: sentence case the title in an article entry.
-Here we get a list of the labels defined as raw latex labels, e.g. \label{eqtre}.
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-get-latex-labels ()
- (save-excursion
- (goto-char (point-min))
- (let ((matches '()))
- (while (re-search-forward "\\\\label{\\([a-zA-z0-9:-]*\\)}" (point-max) t)
- (add-to-list 'matches (match-string-no-properties 1) t))
-matches)))
-#+END_SRC
+- jmax-replace-nonascii :: replace nonascii characters in a bibtex
+ entry. Replacements are in `jmax-nonascii-latex-replacements'. This
+ function is a hook function in org-ref-clean-bibtex-entry.
-Finally, we get the table names.
+The non-ascii characters are looked up in a list of cons cells. You can add your own non-ascii replacements like this. Note backslashes must be escaped doubly, so one \ is \\\\ in the cons cell.
-#+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))))
+#+BEGIN_SRC emacs-lisp
+(add-to-list 'jmax-nonascii-latex-replacements
+ '("æ" . "{\\\\ae}"))
#+END_SRC
-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 and in helm menus."
- (save-excursion
- (save-restriction
- (widen)
- (goto-char (point-min))
- (let ((matches '()))
- ;; 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))))))
-#+END_SRC
+These functions are compatible with bibtex-map-entries, so it is possible to conveniently apply them to all the entries in a file like this:
-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.
-If you are on a label link, replace it."
- (interactive)
- (let* ((labels (org-ref-get-labels))
- (cb (current-buffer)))
- (helm :sources `(((name . "Existing labels")
- (candidates . ,labels)
- ;; default action is to open to the label
- (action . (lambda (label)
- ;; unfortunately I do not have markers here
- (org-open-link-from-string (format "ref:%s" label))))
- ;; if you select a label, replace current one
- (action . (lambda (label)
- (switch-to-buffer ,cb)
- (cond
- ;; no prefix or on a link
- ((equal helm-current-prefix-arg nil)
- (let* ((object (org-element-context))
- (last-char (save-excursion
- (goto-char (org-element-property :end object))
- (backward-char)
- (if (looking-at " ")
- " "
- ""))))
- (when (-contains? '("label")
- (org-element-property :type object))
- ;; we are on a link, so replace it.
- (setf
- (buffer-substring
- (org-element-property :begin object)
- (org-element-property :end object))
- (concat
- (replace-regexp-in-string
- (org-element-property :path object)
- label
- (org-element-property :raw-link object))
- last-char)))))
- ;; no prefix options defined
- ))))
- ;; no matching selection creates a new label
- ((name . "Create new label")
- (dummy)
- ;; default action creates a new label, or replaces old one
- (action . (lambda (label)
- (switch-to-buffer ,cb)
- (let* ((object (org-element-context))
- (last-char (save-excursion
- (goto-char (org-element-property :end object))
- (backward-char)
- (if (looking-at " ")
- " "
- ""))))
- (if (-contains? '("label")
- (org-element-property :type object))
- ;; we are on a link, so replace it.
- (setf
- (buffer-substring
- (org-element-property :begin object)
- (org-element-property :end object))
- (concat
- (replace-regexp-in-string
- (org-element-property :path object)
- helm-pattern
- (org-element-property :raw-link object))
- last-char))
- ;; new link
- (insert
- (concat
- "label:"
- (or label
- helm-pattern))))))))))))
+#+BEGIN_SRC emacs-lisp
+(bibtex-map-entries 'jmax-title-case-article)
#+END_SRC
-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)
- "Completion function for ref links"
- (let ((label))
- (setq label (completing-read "label: " (org-ref-get-labels)))
- (format "ref:%s" label)))
-#+END_SRC
+*** Bibtex entry navigation
+- jmax-bibtex-next-entry :: bound to M-n
+- jmax-bibtex-previous-entry :: bound to M-p
-Alternatively, you may want to just call a function that inserts a link with completion:
+*** Hydra menus for bibtex entries and files
+- Functions to act on a bibtex entry or file
+ - jmax-bibtex-hydra/body :: gives a hydra menu to a lot of useful functions
+ like opening the pdf, or the entry in a browser, or searching in a
+ variety of scientific search engines.
+ - jmax-bibtex-new-entry/body :: gives a hydra menu to add new bibtex entries.
+ - jmax-bibtex-file/body :: gives a hydra menu of actions for the bibtex file.
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-insert-ref-link ()
- (interactive)
- (insert (org-ref-complete-link)))
-#+END_SRC
+You will want to bind the hydra menus to a key. You only need to bind the first one, as the second and third can be accessed from the first hydra.
+You can do that like this before you require jmax-bibtex:
-Another alternative ref insertion is to use helm.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-helm-insert-ref-link ()
- "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))
- (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)
- :sources `(((name . "Available labels to ref")
- (candidates . ,(loop for label in labels
- for context in contexts
- ;; we do some kludgy adding spaces
- ;; and bars to make it "easier" to
- ;; see in helm.
- collect (cons (concat
- label "\n"
- (mapconcat
- (lambda (x)
- (concat " |" x))
- (split-string context "\n")
- "\n"
- ) "\n\n") label)))
- ;; default action to replace or insert ref link.
- (action . (lambda (label)
- (switch-to-buffer ,cb)
-
- (cond
- ;; no prefix or on a link
- ((equal helm-current-prefix-arg nil)
- (let* ((object (org-element-context))
- (last-char (save-excursion
- (goto-char (org-element-property :end object))
- (backward-char)
- (if (looking-at " ")
- " "
- ""))))
- (if (-contains? '("ref" "eqref" "pageref" "nameref")
- (org-element-property :type object))
- ;; we are on a link, so replace it.
- (setf
- (buffer-substring
- (org-element-property :begin object)
- (org-element-property :end object))
- (concat
- (replace-regexp-in-string
- (org-element-property :path object)
- label
- (org-element-property :raw-link object))
- last-char))
- ;; insert a new link
- (insert
- (concat
- "ref:" label))
- )))
- ;; one prefix, alternate ref link
- ((equal helm-current-prefix-arg '(4))
- (insert
- (concat
- (helm :sources '((name . "Ref link types")
- (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)))
- ))
- ))))))
+#+BEGIN_SRC emacs-lisp
+(setq jmax-bibtex-hydra-key-binding "\C-cj")
#+END_SRC
-#+RESULTS:
-: org-ref-helm-insert-ref-link
-
-** pageref
-
-This refers to the page of a label in LaTeX.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(org-add-link-type
- "pageref"
- (lambda (label)
- "on clicking goto the label. Navigate back with C-c &"
- (org-mark-ring-push)
- ;; next search from beginning of the buffer
- (widen)
- (unless
- (or
- ;; our label links
- (progn
- (goto-char (point-min))
- (re-search-forward (format "label:%s\\b" label) nil t))
-
- ;; a latex label
- (progn
- (goto-char (point-min))
- (re-search-forward (format "\\label{%s}" label) nil t))
-
- ;; #+label: name org-definition
- (progn
- (goto-char (point-min))
- (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
-
- ;; org tblname
- (progn
- (goto-char (point-min))
- (re-search-forward (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t))
-
-;; Commented out because these ref links do not actually translate correctly in LaTeX.
-;; you need [[#label]] links.
- ;; CUSTOM_ID
-; (progn
-; (goto-char (point-min))
-; (re-search-forward (format ":CUSTOM_ID:\s-*\\(%s\\)" label) nil t))
- )
- ;; we did not find anything, so go back to where we came
- (org-mark-ring-goto)
- (error "%s not found" label))
- (message "go back with (org-mark-ring-goto) `C-c &`"))
- ;formatting
- (lambda (keyword desc format)
- (cond
- ((eq format 'html) (format "(<pageref>%s</pageref>)" path))
- ((eq format 'latex)
- (format "\\pageref{%s}" keyword)))))
-#+END_SRC
+Or this if you like key-chord:
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-pageref-complete-link (&optional arg)
- "Completion function for ref links"
- (let ((label))
- (setq label (completing-read "label: " (org-ref-get-labels)))
- (format "ref:%s" label)))
+#+BEGIN_SRC emacs-lisp
+(key-chord-define-global "jj" 'jmax-bibtex-hydra/body)
#+END_SRC
-Alternatively, you may want to just call a function that inserts a link with completion:
+** wos
+This is a small utility for Web of Science/Knowledge (http://apps.webofknowledge.com).
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-pageref-insert-ref-link ()
- (interactive)
- (insert (org-pageref-complete-link)))
+#+BEGIN_SRC emacs-lisp
+(require 'wos)
#+END_SRC
-** nameref
-
-The nameref link allows you make links to the text of a section with a label. Clicking on the link takes you to the label, and provides a mark to go back to. This only works if you put a raw latex label in the headline.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(org-add-link-type
- "nameref"
- (lambda (label)
- "on clicking goto the label. Navigate back with C-c &"
- (org-mark-ring-push)
- ;; next search from beginning of the buffer
- (widen)
- (unless
- (or
- ;; a latex label
- (progn
- (goto-char (point-min))
- (re-search-forward (format "\\label{%s}" label) nil t))
- )
- ;; we did not find anything, so go back to where we came
- (org-mark-ring-goto)
- (error "%s not found" label))
- (message "go back with (org-mark-ring-goto) `C-c &`"))
- ;formatting
- (lambda (keyword desc format)
- (cond
- ((eq format 'html) (format "(<nameref>%s</nameref>)" path))
- ((eq format 'latex)
- (format "\\nameref{%s}" keyword)))))
-#+END_SRC
+- wos :: Convenience function to open WOK in a browser.
+- wos-search :: Search WOK with the selected text or word at point
-** eqref
-This is just the LaTeX ref for equations. On export, the reference is enclosed in parentheses.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(org-add-link-type
- "eqref"
- (lambda (label)
- "on clicking goto the label. Navigate back with C-c &"
- (org-mark-ring-push)
- ;; next search from beginning of the buffer
- (widen)
- (goto-char (point-min))
- (unless
- (or
- ;; search forward for the first match
- ;; our label links
- (re-search-forward (format "label:%s" label) nil t)
- ;; a latex label
- (re-search-forward (format "\\label{%s}" label) nil t)
- ;; #+label: name org-definition
- (re-search-forward (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t))
- (org-mark-ring-goto)
- (error "%s not found" label))
- (message "go back with (org-mark-ring-goto) `C-c &`"))
- ;formatting
- (lambda (keyword desc format)
- (cond
- ((eq format 'html) (format "(<eqref>%s</eqref>)" path))
- ((eq format 'latex)
- (format "\\eqref{%s}" keyword)))))
-#+END_SRC
+There is also a new org-mode link that opens a search: [[wos-search:alloy and segregation]]
-** cite
-This is the main reason this library exists. We want the following behavior. A cite link should be able to contain multiple bibtex keys. You should be able to click on the link, and get a brief citation of the entry for that key, and a menu of options to open the bibtex file, open a pdf if you have it, open your notes on the entry, or open a url if it exists. You should be able to insert new references onto an existing cite link, or create new ones easily. The following code implements these features.
-
-*** Implementing the click actions of cite
-
-**** Getting the key we clicked on
-The first thing we need is to get the bibtex key we clicked on.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-get-bibtex-key-under-cursor ()
- "returns key under the bibtex cursor. We search forward from
-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
- ;; sure to move to the beginning so you get the first citation.
- (let ((cp (point)))
- (goto-char (org-element-property :begin object))
- (search-forward link-string (org-element-property :end object))
- (goto-char (match-beginning 0))
- ;; check if we clicked before the path and move as needed.
- (unless (< cp (point))
- (goto-char cp)))
-
- (if (not (org-element-property :contents-begin object))
- ;; this means no description in the link
- (progn
- ;; we need the link path start and end
- (save-excursion
- (goto-char (org-element-property :begin object))
- (search-forward link-string nil nil 1)
- (setq link-string-beginning (match-beginning 0))
- (setq link-string-end (match-end 0)))
-
- ;; The key is the text between commas, or the link boundaries
- (save-excursion
- (if (search-forward "," link-string-end t 1)
- (setq key-end (- (match-end 0) 1)) ; we found a match
- (setq key-end link-string-end))) ; no comma found so take the end
- ;; and backward to previous comma from point which defines the start character
- (save-excursion
- (if (search-backward "," link-string-beginning 1 1)
- (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
- (setq key-beginning link-string-beginning))) ; no match found
- ;; save the key we clicked on.
- (setq bibtex-key (org-ref-strip-string (buffer-substring key-beginning key-end)))
- (set-text-properties 0 (length bibtex-key) nil bibtex-key)
- bibtex-key)
- ;; link with description. assume only one key
- link-string)))
-#+END_SRC
+** isbn
+index:isbn
-We also need to find which bibliography file that key is in. For that, we need to know which bibliography files are referred to in the file. If none are specified with a bibliography link, we use the default bibliography. This function searches for a bibliography link, and then the LaTeX bibliography link. We also consider the addbibresource link which is used with biblatex.
-
-**** Getting the bibliographies
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-find-bibliography ()
- "find the bibliography in the buffer.
-This function sets and returns cite-bibliography-files, which is a list of files
-either from bibliography:f1.bib,f2.bib
-\bibliography{f1,f2}
-internal bibliographies
-
-falling back to what the user has set in org-ref-default-bibliography
-"
- (interactive)
- (catch 'result
- (save-excursion
- (goto-char (point-min))
- ;; look for a bibliography link
- (when (re-search-forward "\\<bibliography:\\([^\]\|\n]+\\)" nil t)
- (setq org-ref-bibliography-files
- (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
- (throw 'result org-ref-bibliography-files))
-
-
- ;; we did not find a bibliography link. now look for \bibliography
- (goto-char (point-min))
- (when (re-search-forward "\\\\bibliography{\\([^}]+\\)}" nil t)
- ;; split, and add .bib to each file
- (setq org-ref-bibliography-files
- (mapcar (lambda (x) (concat x ".bib"))
- (mapcar 'org-ref-strip-string
- (split-string (match-string 1) ","))))
- (throw 'result org-ref-bibliography-files))
-
- ;; no bibliography found. maybe we need a biblatex addbibresource
- (goto-char (point-min))
- ;; look for a bibliography link
- (when (re-search-forward "addbibresource:\\([^\]\|\n]+\\)" nil t)
- (setq org-ref-bibliography-files
- (mapcar 'org-ref-strip-string (split-string (match-string 1) ",")))
- (throw 'result org-ref-bibliography-files))
-
- ;; we did not find anything. use defaults
- (setq org-ref-bibliography-files org-ref-default-bibliography)))
-
- ;; set reftex-default-bibliography so we can search
- (set (make-local-variable 'reftex-default-bibliography) org-ref-bibliography-files)
- org-ref-bibliography-files)
+#+BEGIN_SRC emacs-lisp
+(require 'isbn)
#+END_SRC
-**** Finding the bibliography file a key is in
-Now, we can see if an entry is in a file.
+This library provides some functions to get bibtex entries for books from their ISBN.
-#+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)))
- (bibtex-search-entry key t))))
-#+END_SRC
+- isbn-to-bibtex
-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
- (setq key (org-ref-get-bibtex-key-under-cursor)))
- (setq file (catch 'result
- (loop for file in org-ref-bibliography-files do
- (if (org-ref-key-in-file-p key (file-truename file))
- (throw 'result file)))))
- (cons key file)))
-#+END_SRC
+** pubmed
+index:pubmed
-**** convenience functions to act on citation at point
- :PROPERTIES:
- :ID: af0b2a82-a7c9-4c08-9dac-09f93abc4a92
- :END:
-We need some convenience functions to open act on the citation at point. These will get the pdf, open the url, or open the notes.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-open-pdf-at-point ()
- "open the pdf for bibtex key under point if it exists"
- (interactive)
- (let* ((results (org-ref-get-bibtex-key-and-file))
- (key (car results))
- (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key)))
- (if (file-exists-p pdf-file)
- (org-open-file pdf-file)
-(message "no pdf found for %s" key))))
-
-
-(defun org-ref-open-url-at-point ()
- "open the url for bibtex key under point."
- (interactive)
- (let* ((results (org-ref-get-bibtex-key-and-file))
- (key (car results))
- (bibfile (cdr results)))
- (save-excursion
- (with-temp-buffer
- (insert-file-contents bibfile)
- (bibtex-search-entry key)
- ;; I like this better than bibtex-url which does not always find
- ;; the urls
- (catch 'done
- (let ((url (bibtex-autokey-get-field "url")))
- (when url
- (browse-url 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)))
- (throw 'done nil))))))))
-
-
-(defun org-ref-open-notes-at-point ()
- "open the notes for bibtex key under point."
- (interactive)
- (let* ((results (org-ref-get-bibtex-key-and-file))
- (key (car results))
- (bibfile (cdr results)))
- (save-excursion
- (with-temp-buffer
- (insert-file-contents bibfile)
- (bibtex-search-entry key)
- (org-ref-open-bibtex-notes)))))
-
-
-(defun org-ref-citation-at-point ()
- "give message of current citation at point"
- (interactive)
- (let* ((cb (current-buffer))
- (results (org-ref-get-bibtex-key-and-file))
- (key (car results))
- (bibfile (cdr results)))
- (message "%s" (progn
- (with-temp-buffer
- (insert-file-contents bibfile)
- (bibtex-search-entry key)
- (org-ref-bib-citation))))))
-
-
-(defun org-ref-open-citation-at-point ()
- "open bibtex file to key at point"
- (interactive)
- (let* ((cb (current-buffer))
- (results (org-ref-get-bibtex-key-and-file))
- (key (car results))
- (bibfile (cdr results)))
- (find-file bibfile)
- (bibtex-search-entry key)))
+#+BEGIN_SRC emacs-lisp
+(require 'pubmed)
#+END_SRC
-**** the actual minibuffer menu
-Now, we create the menu. This is a rewrite of the cite action. This makes the function extendable by users.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defvar org-ref-cite-menu-funcs '()
- "Functions to run on cite click menu. Each entry is a list of (key menu-name function).
-The function must take no arguments and work on the key at point. Do not modify this variable, it is set to empty in the menu click function, and functions are conditionally added to it.")
-
-
-(defvar org-ref-user-cite-menu-funcs
- '(("C" "rossref" org-ref-crossref-at-point)
- ("y" "Copy entry to file" org-ref-copy-entry-at-point-to-file)
- ("s" "Copy summary" org-ref-copy-entry-as-summary))
- "user-defined functions to run on bibtex key at point.")
-
-
-(defun org-ref-copy-entry-as-summary ()
- "Copy the bibtex entry for the citation at point as a summary."
- (interactive)
- (save-window-excursion
- (org-ref-open-citation-at-point)
- (kill-new (org-ref-bib-citation))))
-
-
-(defun org-ref-copy-entry-at-point-to-file ()
- "Copy the bibtex entry for the citation at point to NEW-FILE.
-Prompt for NEW-FILE includes bib files in org-ref-default-bibliography, and bib files in current working directory. You can also specify a new file."
- (interactive)
- (let ((new-file (ido-completing-read
- "Copy to bibfile: "
- (append org-ref-default-bibliography
- (f-entries "." (lambda (f) (f-ext? f "bib"))))))
- (key (org-ref-get-bibtex-key-under-cursor)))
- (save-window-excursion
- (org-ref-open-citation-at-point)
- (bibtex-copy-entry-as-kill))
-
- (let ((bibtex-files (list (file-truename new-file))))
- (if (assoc key (bibtex-global-key-alist))
- (message "That key already exists in %s" new-file)
- ;; add to file
- (save-window-excursion
- (find-file new-file)
- (goto-char (point-max))
- ;; make sure we are at the beginning of a line.
- (unless (looking-at "^") (insert "\n\n"))
- (bibtex-yank)
- (save-buffer))))))
-
-
-(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))
- doi)
- (save-excursion
- (with-temp-buffer
- (insert-file-contents bibfile)
- (bibtex-search-entry key)
- (setq doi (bibtex-autokey-get-field "doi"))
- ;; in case doi is a url, remove the url part.
- (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))))
-
-
-;; functions that operate on key at point for click menu
-(defun org-ref-wos-at-point ()
- "open the doi in wos for bibtex key under point."
- (interactive)
- (doi-utils-wos (org-ref-get-doi-at-point)))
-
-
-(defun org-ref-wos-citing-at-point ()
- "open the doi in wos citing articles for bibtex key under point."
- (interactive)
- (doi-utils-wos-citing (org-ref-get-doi-at-point)))
-
-
-(defun org-ref-wos-related-at-point ()
- "open the doi in wos related articles for bibtex key under point."
- (interactive)
- (doi-utils-wos-related (org-ref-get-doi-at-point)))
-
-
-(defun org-ref-google-scholar-at-point ()
- "open the doi in google scholar for bibtex key under point."
- (interactive)
- (doi-utils-google-scholar (org-ref-get-doi-at-point)))
-
-
-(defun org-ref-pubmed-at-point ()
- "open the doi in pubmed for bibtex key under point."
- (interactive)
- (doi-utils-pubmed (org-ref-get-doi-at-point)))
-
-
-(defun org-ref-crossref-at-point ()
- "open the doi in crossref for bibtex key under point."
- (interactive)
- (doi-utils-crossref (org-ref-get-doi-at-point)))
-
-
-(defun org-ref-cite-onclick-minibuffer-menu (&optional link-string)
- "action when a cite link is clicked on.
-Provides a menu of context sensitive actions. If the bibtex entry has a pdf, you get an option to open it. If there is a doi, you get a lot of options."
- (interactive)
- (let* ((results (org-ref-get-bibtex-key-and-file))
- (key (car results))
- (pdf-file (format (concat org-ref-pdf-directory "%s.pdf") key))
- (bibfile (cdr results))
- (url (save-excursion
- (with-temp-buffer
- (insert-file-contents bibfile)
- (bibtex-search-entry key)
- (bibtex-autokey-get-field "url"))))
- (doi (save-excursion
- (with-temp-buffer
- (insert-file-contents bibfile)
- (bibtex-search-entry key)
- ;; I like this better than bibtex-url which does not always find
- ;; the urls
- (bibtex-autokey-get-field "doi")))))
-
- (when (string= "" doi) (setq doi nil))
- (when (string= "" url) (setq url nil))
- (setq org-ref-cite-menu-funcs '())
-
- ;; open action
- (when
- bibfile
- (add-to-list
- 'org-ref-cite-menu-funcs
- '("o" "pen" org-ref-open-citation-at-point)))
-
- ;; pdf
- (when (file-exists-p pdf-file)
- (add-to-list
- 'org-ref-cite-menu-funcs
- `("p" "df" ,org-ref-open-pdf-function) t))
-
- ;; notes
- (add-to-list
- 'org-ref-cite-menu-funcs
- '("n" "otes" org-ref-open-notes-at-point) t)
-
- ;; url
- (when (or url doi)
- (add-to-list
- 'org-ref-cite-menu-funcs
- '("u" "rl" org-ref-open-url-at-point) t))
-
- ;; doi funcs
- (when doi
- (add-to-list
- 'org-ref-cite-menu-funcs
- '("w" "os" org-ref-wos-at-point) t)
-
- (add-to-list
- 'org-ref-cite-menu-funcs
- '("c" "iting" org-ref-wos-citing-at-point) t)
-
- (add-to-list
- 'org-ref-cite-menu-funcs
- '("r" "elated" org-ref-wos-related-at-point) t)
-
- (add-to-list
- 'org-ref-cite-menu-funcs
- '("g" "oogle scholar" org-ref-google-scholar-at-point) t)
-
- (add-to-list
- 'org-ref-cite-menu-funcs
- '("P" "ubmed" org-ref-pubmed-at-point) t))
-
- ;; add user functions
- (dolist (tup org-ref-user-cite-menu-funcs)
- (add-to-list
- 'org-ref-cite-menu-funcs
- tup t))
-
- ;; finally quit
- (add-to-list
- 'org-ref-cite-menu-funcs
- '("q" "uit" (lambda ())) t)
-
- ;; now we make a menu
- ;; construct menu string as a message
- (message
- (concat
- (let* ((results (org-ref-get-bibtex-key-and-file))
- (key (car results))
- (bibfile (cdr results)))
- (save-excursion
- (with-temp-buffer
- (insert-file-contents bibfile)
- (bibtex-search-entry key)
- (org-ref-bib-citation))))
- "\n"
- (mapconcat
- (lambda (tup)
- (concat "[" (elt tup 0) "]"
- (elt tup 1) " "))
- org-ref-cite-menu-funcs "")))
- ;; get the input
- (let* ((input (read-char-exclusive))
- (choice (assoc
- (char-to-string input) org-ref-cite-menu-funcs)))
- ;; now run the function (2nd element in choice)
- (when choice
- (funcall
- (elt
- choice
- 2))))))
-#+END_SRC
+This library provides a number of new org-mode links to Pubmed entries. See http://www.ncbi.nlm.nih.gov/pmc/about/public-access-info/#p3 for details of these identifiers.
-#+RESULTS:
-: org-ref-cite-onclick-minibuffer-menu
+pmcid:PMC3498956
-*** A function to format a cite link
+pmid:23162369
-Next, we define a formatting function for the cite link. This is done so that the cite link definition is very short, and easy to change. You just need to specify the functions in the definition. This function is deprecated. The formatting is defined later automatically.
+nihmsid:NIHMS395714
-#+BEGIN_SRC emacs-lisp :tangle no
-;(defun org-ref-cite-link-format (keyword desc format)
-; (cond
-; ((eq format 'html) (mapconcat (lambda (key) (format "<a name=\"#%s\">%s</a>" key key) (org-ref-split-and-strip-string keyword) ",")))
-; ((eq format 'latex)
-; (concat "\\cite" (when desc (format "[%s]" desc)) "{"
-; (mapconcat (lambda (key) key) (org-ref-split-and-strip-string keyword) ",")
-; "}"))))
-#+END_SRC
+Also, you can retrieve a bibtex entry for a PMID with
-*** The actual cite link
-Finally, we define the cite link. This is deprecated; the links are autogenerated later. This is here for memory.
+- pubmed-insert-bibtex-from-pmid
-#+BEGIN_SRC emacs-lisp :tangle no
-;(org-add-link-type
-; "cite"
-; 'org-ref-cite-onclick-minibuffer-menu
-; 'org-ref-cite-link-format)
-#+END_SRC
+** arxiv
+index:arxiv
-*** Automatic definition of the cite links
-There are many different kinds of citations in LaTeX, but they are all variants of a basic syntax of \citetype[optional text]{label1,label2}. Here we use lisp to generate the link definitions. We define a function that creates the code to create the link, and then we evaluate it. We also create the completion function for the new link, and add it to the list of known links.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defmacro org-ref-make-completion-function (type)
- `(defun ,(intern (format "org-%s-complete-link" type)) (&optional arg)
- (interactive)
- (format "%s:%s"
- ,type
- (completing-read
- "bibtex key: "
- (let ((bibtex-files (org-ref-find-bibliography)))
- (bibtex-global-key-alist))))))
-#+END_SRC
+This library provides an org-mode link to http://arxiv.org entries: arxiv:cond-mat/0410285, and a function to get a bibtex entry and pdfs for arxiv entries:
-We will want to generate formatting functions for each citation type. The reason for doing this is so we can on the fly change the formatting later.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defmacro org-ref-make-format-function (type)
- `(defun ,(intern (format "org-ref-format-%s" type)) (keyword desc format)
- (cond
- ((eq format 'org)
- (mapconcat
- (lambda (key)
- (format "[[#%s][%s]]" key key))
- (org-ref-split-and-strip-string keyword) ","))
-
- ((eq format 'ascii)
- (concat "["
- (mapconcat
- (lambda (key)
- (format "%s" key))
- (org-ref-split-and-strip-string keyword) ",") "]"))
-
- ((eq format 'html)
- (mapconcat
- (lambda (key)
- (format "<a href=\"#%s\">%s</a>" key key))
- (org-ref-split-and-strip-string keyword) ","))
-
- ((eq format 'latex)
- (if (string= (substring type -1) "s")
- ;; biblatex format for multicite commands, which all end in s. These are formated as \cites{key1}{key2}...
- (concat "\\" ,type (mapconcat (lambda (key) (format "{%s}" key))
- (org-ref-split-and-strip-string keyword) ""))
- ;; 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)
- "; "))))))))
+#+BEGIN_SRC emacs-lisp
+(require 'arxiv)
#+END_SRC
+- arxiv-add-bibtex-entry
+- arxiv-get-pdf
+** sci-id
+index:orcid [[index:researcher id]]
-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)
- (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:
-(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: ")
-
- ;; create the formatting function
- (eval `(org-ref-make-format-function ,type))
-
- (eval-expression
- `(org-add-link-type
- ,type
- org-ref-cite-onclick-function
- (quote ,(intern (format "org-ref-format-%s" type)))))
-
- ;; create the completion function
- (eval `(org-ref-make-completion-function ,type))
-
- ;; store new type so it works with adding citations, which checks
- ;; for existence in this list
- (add-to-list 'org-ref-cite-types type)
-
- ;; and finally if a key is specified, we modify the reftex menu
- (when key
- (setf (nth 2 (assoc 'org reftex-cite-format-builtin))
- (append (nth 2 (assoc 'org reftex-cite-format-builtin))
- `((,key . ,(concat type ":%l")))))))
-
-;; create all the link types and their completion functions
-(mapcar 'org-ref-define-citation-link org-ref-cite-types)
-#+END_SRC
-
-*** 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
-(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
-inserted. Use a prefix arg to get a menu of citation types."
- (interactive "P")
- (org-ref-find-bibliography)
- (let* ((object (org-element-context))
- (link-string-beginning (org-element-property :begin object))
- (link-string-end (org-element-property :end object))
- (path (org-element-property :path object)))
-
- (if (not alternative-cite)
-
- (cond
- ;; case where we are in a link
- ((and (equal (org-element-type object) 'link)
- (-contains? org-ref-cite-types (org-element-property :type object)))
- (goto-char link-string-end)
- ;; sometimes there are spaces at the end of the link
- ;; this code moves point pack until no spaces are there
- (while (looking-back " ") (backward-char))
- (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
-
- ;; We are next to a link, and we want to append
- ((save-excursion
- (backward-char)
- (and (equal (org-element-type (org-element-context)) 'link)
- (-contains? org-ref-cite-types (org-element-property :type (org-element-context)))))
- (while (looking-back " ") (backward-char))
- (insert (concat "," (mapconcat 'identity (reftex-citation t ?a) ","))))
-
- ;; insert fresh link
- (t
- (insert
- (concat org-ref-default-citation-link
- ":"
- (mapconcat 'identity (reftex-citation t) ",")))))
-
- ;; you pressed a C-u so we run this code
- (reftex-citation)))
- )
+#+BEGIN_SRC emacs-lisp
+(require 'sci-id)
#+END_SRC
-cite:zhou-2004-first-lda-u,paier-2006-errat,boes-2015-estim-bulk
+This package just defines two new org-mode links for http://www.orcid.org, and http://www.researcherid.com. Here are two examples:
-#+RESULTS:
-: org-ref-insert-cite-link
-
-*** Completion in cite links
-If you know the specific bibtex key, you may like to use completion directly. You use this with the org-mode machinery and tab completion. Here is the prototypical completion function. These are now all created when the links are created.
-
-#+BEGIN_SRC emacs-lisp :tangle no
-(defun org-cite-complete-link (&optional arg)
- "Completion function for cite links"
- (format "%s:%s"
- org-ref-default-citation-link
- (completing-read
- "bibtex key: "
- (let ((bibtex-files (org-ref-find-bibliography)))
- (bibtex-global-key-alist)))))
-#+END_SRC
+orcid:0000-0003-2625-9232
-Alternatively, you may shortcut the org-machinery with this command. You will be prompted for a citation type, and then offered key completion.
+researcherid:A-2363-2010
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-insert-cite-with-completion (type)
- "Insert a cite link with completion"
- (interactive (list (ido-completing-read "Type: " org-ref-cite-types)))
- (insert (funcall (intern (format "org-%s-complete-link" type)))))
-#+END_SRC
+** x2bib
+index:bibtex!conversion
-** Storing links to a bibtex entry
-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
-(defun org-ref-store-bibtex-entry-link ()
- "Save a citation link to the current bibtex entry. Saves in the default link type."
- (interactive)
- (let ((link (concat org-ref-default-citation-link
- ":"
- (save-excursion
- (bibtex-beginning-of-entry)
- (reftex-get-bib-field "=key=" (bibtex-parse-entry))))))
- (message "saved %s" link)
- (push (list link) org-stored-links)
- (car org-stored-links)))
+#+BEGIN_SRC emacs-lisp
+(require 'x2bib)
#+END_SRC
-** Index entries
-org-ref minimally supports index entries. To make an index in a file, you should put in the LaTeX header these lines
+If you find you need to convert some bibliographies in some format into bibtex, this library is a starting point. This code is mostly wrappers around the command line utilities at http://sourceforge.net/p/bibutils/home/Bibutils. I thankfully have not had to use this often, but it is here when I need it again.
+- ris2bib :: Convert an RIS file to a bibtex file.
+- medxml2bib :: Convert Pubmed XML to bibtex.
+- clean-entries :: Map over a converted bibtex file and "clean it".
-#+LATEX_HEADER: \usepackage{makeidx}
-#+LATEX_HEADER: \makeindex
-
-
-Finally, put \makeindex at the end of the document where you want the index to appear. You will need to run the makeindex program at an appropriate point in your LaTeX to pdf, or use ox-manuscript, which will do it for you.
-
-
-Use index links to create entries (see http://en.wikibooks.org/wiki/LaTeX/Indexing). Clicking on an index link runs occur on the buffer for the entry. The link exports to LaTeX. Some links may need to be enclosed in double brackets if they have spaces in them.
-
-
-index:hello
-index:hello!Peter
-[[index:hello!Sam@\textsl{Sam}]]
-[[index:Lin@\textbf{Lin}]]
-[[index:Joe|textit]]
-[[index:Lin@\textbf{Lin}]]
-[[index:Peter|see {hello}]]
-[[index:Jen|seealso{Jenny}]]
-
-index:encodings!input!cp850
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(org-add-link-type
- "index"
- (lambda (path)
- (occur path))
-
- (lambda (path desc format)
- (cond
- ((eq format 'latex)
- (format "\\index{%s}" path)))))
-
-;; this will generate a temporary index of entries in the file.
-(org-add-link-type
- "printindex"
- (lambda (path)
- (let ((*index-links* '())
- (*initial-letters* '()))
-
- ;; get links
- (org-element-map (org-element-parse-buffer) 'link
- (lambda (link)
- (let ((type (nth 0 link))
- (plist (nth 1 link)))
-
- (when (equal (plist-get plist ':type) "index")
- (add-to-list
- '*index-links*
- (cons (plist-get plist :path)
- (format
- "[[elisp:(progn (switch-to-buffer \"%s\") (goto-char %s))][%s]]"
-(current-buffer)
- (plist-get plist :begin) ;; position of link
- ;; grab a description
- (save-excursion
- (goto-char (plist-get plist :begin))
- (if (thing-at-point 'sentence)
- ;; get a sentence
- (replace-regexp-in-string
- "\n" "" (thing-at-point 'sentence))
- ;; or call it a link
- "link")))))))))
-
- ;; sort the links
- (setq *index-links* (cl-sort *index-links* 'string-lessp :key 'car))
-
- ;; now first letters
- (dolist (link *index-links*)
- (add-to-list '*initial-letters* (substring (car link) 0 1) t))
-
- ;; now create the index
- (switch-to-buffer (get-buffer-create "*index*"))
- (org-mode)
- (erase-buffer)
- (insert "#+TITLE: Index\n\n")
- (dolist (letter *initial-letters*)
- (insert (format "* %s\n" (upcase letter)))
- ;; now process the links
- (while (and
- ,*index-links*
- (string= letter (substring (car (car *index-links*)) 0 1)))
- (let ((link (pop *index-links*)))
- (insert (format "%s %s\n\n" (car link) (cdr link))))))
- (switch-to-buffer "*index*")))
- ;; formatting
- (lambda (path desc format)
- (cond
- ((eq format 'latex)
- (format "\\printindex")))))
-#+END_SRC
+* Appendix
+** Customizing org-ref
+ :PROPERTIES:
+ :ID: 32B558A3-7B48-4581-982B-082017B0AEE8
+ :END:
+index:customization
-#+RESULTS:
-| lambda | (path) | (let ((*index-links* (quote nil)) (*initial-letters* (quote nil))) (org-element-map (org-element-parse-buffer) (quote link) (lambda (link) (let ((type (nth 0 link)) (plist (nth 1 link))) (when (equal (plist-get plist (quote :type)) index) (add-to-list (quote *index-links*) (cons (plist-get plist :path) (format [[elisp:(progn (switch-to-buffer "%s") (goto-char %s))][%s]] (current-buffer) (plist-get plist :begin) (save-excursion (goto-char (plist-get plist :begin)) (if (thing-at-point (quote sentence)) (replace-regexp-in-string \n (thing-at-point (quote sentence))) link))))))))) (setq *index-links* (cl-sort *index-links* (quote string-lessp) :key (quote car))) (dolist (link *index-links*) (add-to-list (quote *initial-letters*) (substring (car link) 0 1) t)) (switch-to-buffer (get-buffer-create *index*)) (org-mode) (erase-buffer) (insert #+TITLE: Index\n\n) (dolist (letter *initial-letters*) (insert (format * %s\n (upcase letter))) (while (and *index-links* (string= letter (substring (car (car *index-links*)) 0 1))) (let ((link (pop *index-links*))) (insert (format %s %s\n\n (car link) (cdr link)))))) (switch-to-buffer *index*)) |
-| lambda | (path desc format) | (cond ((eq format (quote latex)) (format \printindex))) |
-
-** Glossary
-org-ref provides some minimal support for a glossary. See http://en.wikibooks.org/wiki/LaTeX/Glossary for details. You need to put these lines in the header.
-
-#+LATEX_HEADER: \usepackage{glossaries}
-#+LATEX_HEADER: \makeglossaries
-
-And at the end of the document put \makeglossaries.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(org-add-link-type
- "newglossaryentry"
- nil ;; no follow action
- (lambda (path desc format)
- (cond
- ((eq format 'latex)
- (format "\\newglossaryentry{%s}{%s}" path desc)))))
-
-
-;; link to entry
-(org-add-link-type
- "gls"
- nil ;; no follow action
- (lambda (path desc format)
- (cond
- ((eq format 'latex)
- (format "\\gls{%s}" path)))))
-
-;; plural
-(org-add-link-type
- "glspl"
- nil ;; no follow action
- (lambda (path desc format)
- (cond
- ((eq format 'latex)
- (format "\\glspl{%s}" path)))))
-
-;; capitalized link
-(org-add-link-type
- "Gls"
- nil ;; no follow action
- (lambda (path desc format)
- (cond
- ((eq format 'latex)
- (format "\\Gls{%s}" path)))))
-
-;; capitalized link
-(org-add-link-type
- "Glspl"
- nil ;; no follow action
- (lambda (path desc format)
- (cond
- ((eq format 'latex)
- (format "\\Glspl{%s}" path)))))
-#+END_SRC
+You will probably want to customize a few variables before using org-ref extensively. One way to do this is through the Emacs customization interface: [[elisp:(customize-group "org-ref")]].
-* Utilities
-** create simple text citation from bibtex entry
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-bib-citation ()
- "From a bibtex entry, create and return a simple citation string.
-This assumes you are in an article."
-
- (bibtex-beginning-of-entry)
- (let* ((cb (current-buffer))
- (bibtex-expand-strings t)
- (entry (loop for (key . value) in (bibtex-parse-entry t)
- collect (cons (downcase key) value)))
- (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
- (year (reftex-get-bib-field "year" entry))
- (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
- (key (reftex-get-bib-field "=key=" entry))
- (journal (reftex-get-bib-field "journal" entry))
- (volume (reftex-get-bib-field "volume" entry))
- (pages (reftex-get-bib-field "pages" entry))
- (doi (reftex-get-bib-field "doi" entry))
- (url (reftex-get-bib-field "url" entry))
- )
- ;;authors, "title", Journal, vol(iss):pages (year).
- (format "%s, \"%s\", %s, %s:%s (%s)"
- author title journal volume pages year)))
-#+END_SRC
+Here is my minimal setup:
+#+BEGIN_SRC emacs-lisp
+(setq reftex-default-bibliography '("~/Dropbox/bibliography/references.bib"))
-#+RESULTS:
-: org-ref-bib-citation
-
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-bib-html-citation ()
- "from a bibtex entry, create and return a simple citation with html links."
-
- (bibtex-beginning-of-entry)
- (let* ((cb (current-buffer))
- (bibtex-expand-strings t)
- (entry (loop for (key . value) in (bibtex-parse-entry t)
- collect (cons (downcase key) value)))
- (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
- (year (reftex-get-bib-field "year" entry))
- (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
- (key (reftex-get-bib-field "=key=" entry))
- (journal (reftex-get-bib-field "journal" entry))
- (volume (reftex-get-bib-field "volume" entry))
- (pages (reftex-get-bib-field "pages" entry))
- (doi (reftex-get-bib-field "doi" entry))
- (url (reftex-get-bib-field "url" entry))
- )
- ;;authors, "title", Journal, vol(iss):pages (year).
- (concat (format "%s, \"%s\", %s, %s:%s (%s)."
- author title journal volume pages year)
- (when url (format " <a href=\"%s\">link</a>" url))
- (when doi (format " <a href=\"http://dx.doi.org/%s\">doi</a>" doi)))
- ))
+(setq org-ref-bibliography-notes "~/Dropbox/bibliography/notes.org"
+ org-ref-default-bibliography '("~/Dropbox/bibliography/references.bib")
+ org-ref-pdf-directory "~/Dropbox/bibliography/bibtex-pdfs/")
#+END_SRC
-** 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
-(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."
- (interactive)
- (save-excursion
- (bibtex-beginning-of-entry)
- (let* ((bibtex-expand-strings t)
- (entry (bibtex-parse-entry t))
- (key (reftex-get-bib-field "=key=" entry))
- (pdf (format (concat org-ref-pdf-directory "%s.pdf") key)))
- (message "%s" pdf)
- (if (file-exists-p pdf)
- (org-open-link-from-string (format "[[file:%s]]" pdf))
- (ding)))))
-#+END_SRC
+For jmax-bibtex I like:
-** open notes 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
-(defun org-ref-open-bibtex-notes ()
- "from a bibtex entry, open the notes if they exist, and create a heading if they do not.
-
-I never did figure out how to use reftex to make this happen
-non-interactively. the reftex-format-citation function did not
-work perfectly; there were carriage returns in the strings, and
-it did not put the key where it needed to be. so, below I replace
-the carriage returns and extra spaces with a single space and
-construct the heading by hand."
- (interactive)
-
- (bibtex-beginning-of-entry)
- (let* ((cb (current-buffer))
- (bibtex-expand-strings t)
- (entry (loop for (key . value) in (bibtex-parse-entry t)
- collect (cons (downcase key) value)))
- (title (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "title" entry)))
- (year (reftex-get-bib-field "year" entry))
- (author (replace-regexp-in-string "\n\\|\t\\|\s+" " " (reftex-get-bib-field "author" entry)))
- (key (reftex-get-bib-field "=key=" entry))
- (journal (reftex-get-bib-field "journal" entry))
- (volume (reftex-get-bib-field "volume" entry))
- (pages (reftex-get-bib-field "pages" entry))
- (doi (reftex-get-bib-field "doi" entry))
- (url (reftex-get-bib-field "url" entry))
- )
-
- ;; save key to clipboard to make saving pdf later easier by pasting.
- (with-temp-buffer
- (insert key)
- (kill-ring-save (point-min) (point-max)))
-
- ;; now look for entry in the notes file
- (if org-ref-bibliography-notes
- (find-file-other-window org-ref-bibliography-notes)
- (error "org-ref-bib-bibliography-notes is not set to anything"))
-
- (goto-char (point-min))
- ;; put new entry in notes if we don't find it.
- (if (re-search-forward (format ":Custom_ID: %s$" key) nil 'end)
- (funcall org-ref-open-notes-function)
- ;; no entry found, so add one
- (insert (format "\n** TODO %s - %s" year title))
- (insert (format"
- :PROPERTIES:
- :Custom_ID: %s
- :AUTHOR: %s
- :JOURNAL: %s
- :YEAR: %s
- :VOLUME: %s
- :PAGES: %s
- :DOI: %s
- :URL: %s
- :END:
-[[cite:%s]] [[file:%s/%s.pdf][pdf]]\n\n"
-key author journal year volume pages doi url key org-ref-pdf-directory key))
-(save-buffer))))
+#+BEGIN_SRC emacs-lisp
+(setq jmax-bibtex-hydra-key-chord "jj")
#+END_SRC
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-open-notes-from-reftex ()
- "Call reftex, and open notes for selected entry."
- (interactive)
- (let ((bibtex-key )))
-
- ;; now look for entry in the notes file
- (if org-ref-bibliography-notes
- (find-file-other-window org-ref-bibliography-notes)
- (error "org-ref-bib-bibliography-notes is not set to anything"))
-
- (goto-char (point-min))
+** Other things org-ref supports
+*** org-completion
+index:completion index:link!completion
- (re-search-forward (format
- ":Custom_ID: %s$"
- (first (reftex-citation t)) nil 'end))
- (funcall org-ref-open-notes-function))
-#+END_SRC
+Most org-ref links support org-mode completion. You can type C-c C-l to insert a link. You will get completion of the link type, type some characters and press tab. When you select the type, press tab to see the completion options. This works for the following link types:
-** open url in browser from bibtex
-
-We bind this to a key here [[*key%20bindings%20for%20utilities][key bindings for utilities]].
-
-+ This function may be duplicative of bibtex-url. But I think my function is better unless you do some complicated customization of bibtex-generate-url-list.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-open-in-browser ()
- "Open the bibtex entry at point in a browser using the url field or doi field"
-(interactive)
-(save-excursion
- (bibtex-beginning-of-entry)
- (catch 'done
- (let ((url (bibtex-autokey-get-field "url")))
- (when url
- (browse-url 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)))
- (throw 'done nil)))
- (message "No url or doi found"))))
-#+END_SRC
+- bibliography
+- bibliographystyle
+- all cite types
+- ref
-** citeulike
- I discovered you could upload a bibtex entry to citeulike using http requests. The upload is actually done by a [[*The%20upload%20script][python script]], because it was easy to write. Here is the emacs command to do this. It is not a fast operation, and do not use it frequently.
-
-*** function to upload bibtex to citeulike
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-upload-bibtex-entry-to-citeulike ()
- "with point in a bibtex entry get bibtex string and submit to citeulike.
-
-Relies on the python script /upload_bibtex_citeulike.py being in the user directory."
- (interactive)
- (message "uploading to citeulike")
- (save-restriction
- (bibtex-narrow-to-entry)
- (let ((startpos (point-min))
- (endpos (point-max))
- (bibtex-string (buffer-string))
- (script (concat "python " starter-kit-dir "/upload_bibtex_citeulike.py&")))
- (with-temp-buffer (insert bibtex-string)
- (shell-command-on-region (point-min) (point-max) script t nil nil t)))))
-#+END_SRC
+*** Storing org-links to labels
+ :PROPERTIES:
+ :ID: AD9663C7-1369-413F-842A-157916D4BB75
+ :CUSTOM_ID: sec-store-links
+ :END:
+index:link!storing
-*** The upload script
-Here is the python script for uploading.
+If you are on a label link, or on a table name, or on an org-mode label you can "store" a link to it by typing C-c l. Then you can insert the corresponding ref link with C-c C-l. This will insert a ref link or custom_id link as needed. This usually works, but it is not used by me too often, so it is not tested too deeply.
-*************** TODO document how to get the cookies
-*************** END
+*** Storing links to bibtex entries
+If you have a bibtex file open, you type C-c C-l with your cursor in a bibtex entry to store a link to that entry. In an org-buffer if you then type C-c l, you can enter a cite link.
-# :tangle upload_bibtex_citeulike.py
-#+BEGIN_SRC python
-#!python
-import pickle, requests, sys
+*** Indexes
+index:index
-# reload cookies
-with open('c:/Users/jkitchin/Dropbox/blogofile-jkitchin.github.com/_blog/cookies.pckl', 'rb') as f:
- cookies = pickle.load(f)
+org-ref provides links to support making an index in LaTeX. (http://en.wikibooks.org/wiki/LaTeX/Indexing).
-url = 'http://www.citeulike.org/profile/jkitchin/import_do'
+- index :: creates an index entry.
+- printindex :: Generates a temporary index of clickable entries. Exports to the LaTeX command.
-bibtex = sys.stdin.read()
+You will need to use the makeidx package, and use this in the LaTeX header.
-data = {'pasted':bibtex,
- 'to_read':2,
- 'tag_parsing':'simple',
- 'strip_brackets':'no',
- 'update_id':'bib-key',
- 'btn_bibtex':'Import BibTeX file ...'}
+#+LATEX_HEADER: \usepackage{makeidx}
+#+LATEX_HEADER: \makeindex
-headers = {'content-type': 'multipart/form-data',
- 'User-Agent':'jkitchin/johnrkitchin@gmail.com bibtexupload'}
+You will have to incorporate running makeindex into your PDF build command.
-r = requests.post(url, headers=headers, data=data, cookies=cookies, files={})
-print r
-#+END_SRC
+This is not supported in anything but LaTeX export.
-** Build a pdf from a bibtex file
- It is useful to have a pdf version of an entire bibliography to check it for formatting, spelling, or to share it. This function creates a pdf from a bibtex file. I only include the packages I commonly use in my bitex files.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-build-full-bibliography ()
- "build pdf of all bibtex entries, and open it."
- (interactive)
- (let* ((bibfile (file-name-nondirectory (buffer-file-name)))
- (bib-base (file-name-sans-extension bibfile))
- (texfile (concat bib-base ".tex"))
- (pdffile (concat bib-base ".pdf")))
- (find-file texfile)
- (erase-buffer)
- (insert (format "\\documentclass[12pt]{article}
-\\usepackage[version=3]{mhchem}
-\\usepackage{url}
-\\usepackage[numbers]{natbib}
-\\usepackage[colorlinks=true, linkcolor=blue, urlcolor=blue, pdfstartview=FitH]{hyperref}
-\\usepackage{doi}
-\\begin{document}
-\\nocite{*}
-\\bibliographystyle{unsrtnat}
-\\bibliography{%s}
-\\end{document}" bib-base))
- (save-buffer)
- (shell-command (concat "pdflatex " bib-base))
- (shell-command (concat "bibtex " bib-base))
- (shell-command (concat "pdflatex " bib-base))
- (shell-command (concat "pdflatex " bib-base))
- (kill-buffer texfile)
- (org-open-file pdffile)
- ))
-#+END_SRC
+*** Glossaries
+index:glossary
-** Extract bibtex entries cited in an org-file
-When you use your default bibliography file, and you want to send an org-file to a collaborator, you may need to include bibtex entries so the other person can see them. This function does that and puts the entries in a section at the end of the document that can be tangled to a bib-file.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-extract-bibtex-entries ()
- "extract the bibtex entries referred to by cite links in the current buffer into a src block at the bottom of the current buffer.
-
-If no bibliography is in the buffer the `reftex-default-bibliography' is used."
- (interactive)
- (let* ((temporary-file-directory (file-name-directory (buffer-file-name)))
- (tempname (make-temp-file "extract-bib"))
- (contents (buffer-string))
- (cb (current-buffer))
- basename texfile bibfile results)
-
- ;; open tempfile and insert org-buffer contents
- (find-file tempname)
- (insert contents)
- (setq basename (file-name-sans-extension
- (file-name-nondirectory buffer-file-name))
- texfile (concat tempname ".tex")
- bibfile (concat tempname ".bib"))
-
- ;; see if we have a bibliography, and insert the default one if not.
- (save-excursion
- (goto-char (point-min))
- (unless (re-search-forward "^bibliography:" (point-max) 'end)
- (insert (format "\nbibliography:%s"
- (mapconcat 'identity reftex-default-bibliography ",")))))
- (save-buffer)
-
- ;; get a latex file and extract the references
- (org-latex-export-to-latex)
- (find-file texfile)
- (reftex-parse-all)
- (reftex-create-bibtex-file bibfile)
- (save-buffer)
- ;; save results of the references
- (setq results (buffer-string))
-
- ;; kill buffers. these are named by basename, not full path
- (kill-buffer (concat basename ".bib"))
- (kill-buffer (concat basename ".tex"))
- (kill-buffer basename)
-
- (delete-file bibfile)
- (delete-file texfile)
- (delete-file tempname)
-
- ;; Now back to the original org buffer and insert the results
- (switch-to-buffer cb)
- (when (not (string= "" results))
- (save-excursion
- (goto-char (point-max))
- (insert "\n\n")
- (org-insert-heading)
- (insert (format " Bibtex entries
-
-,#+BEGIN_SRC text :tangle %s
-%s
-,#+END_SRC" (concat (file-name-sans-extension (file-name-nondirectory (buffer-file-name))) ".bib") results))))))
-#+END_SRC
+See http://en.wikibooks.org/wiki/LaTeX/Glossary. Not all options are supported. I have never actually used this functionality.
-** Find bad cite links
- :PROPERTIES:
- :ID: 8515E800-EDA0-4B2A-85FD-55B6FF849203
- :END:
-Depending on how you enter citations, you may have citations with no corresponding bibtex entry. This function finds them and gives you a clickable table to navigate to them.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(require 'cl)
-
-(defun index (substring list)
- "return the index of string in a list of strings"
- (let ((i 0)
- (found nil))
- (dolist (arg list i)
- (if (string-match (concat "^" substring "$") arg)
- (progn
- (setq found t)
- (return i)))
- (setq i (+ i 1)))
- ;; return counter if found, otherwise return nil
- (if found i nil)))
-
-
-(defun org-ref-find-bad-citations ()
- "Create a list of citation keys in an org-file that do not have a bibtex entry in the known bibtex files.
-
-Makes a new buffer with clickable links."
- (interactive)
- ;; generate the list of bibtex-keys and cited keys
- (let* ((bibtex-files (org-ref-find-bibliography))
- (bibtex-file-path (mapconcat (lambda (x) (file-name-directory (file-truename x))) bibtex-files ":"))
- (bibtex-keys (mapcar (lambda (x) (car x)) (bibtex-global-key-alist)))
- (bad-citations '()))
-
- (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 (not (index key bibtex-keys))
- (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
- (switch-to-buffer-other-window "*Missing citations*")
- (org-mode)
- (erase-buffer)
- (insert "* List of bad cite links\n")
- (insert (mapconcat 'identity bad-citations ""))
- ;(setq buffer-read-only t)
- (use-local-map (copy-keymap org-mode-map))
- (local-set-key "q" #'(lambda () (interactive) (kill-buffer))))
-
- (when (get-buffer "*Missing citations*")
- (kill-buffer "*Missing citations*"))
- (message "No bad cite links found"))))
-#+END_SRC
-
-** helm interface to org-ref
-In [[id:8515E800-EDA0-4B2A-85FD-55B6FF849203][Find bad cite links]] we wrote a function that finds bad links and creates a buffer of links to them.
-
-Here we develop a similar idea, but instead of an org-buffer with links, we create helm sources for bad cite links, bad ref links, and multiple labels.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-bad-cite-candidates ()
- "Returns a list of conses (key . marker) where key does not exist in the known bibliography files, and marker points to the key."
- (let* ((cp (point)) ; save to return to later
- (bibtex-files (org-ref-find-bibliography))
- (bibtex-file-path (mapconcat
- (lambda (x)
- (file-name-directory (file-truename x)))
- bibtex-files ":"))
- (bibtex-keys (mapcar (lambda (x) (car x))
- (bibtex-global-key-alist)))
- (bad-citations '()))
-
- (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 (not (index key bibtex-keys))
- (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))
-
-
-(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)."
- ;; first get a list of legitimate labels
- (let ((cp (point))
- (labels (org-ref-get-labels))
- (bad-refs '()))
- ;; now loop over ref links
- (goto-char (point-min))
- (org-element-map (org-element-parse-buffer) 'link
- (lambda (link)
- (let ((plist (nth 1 link)))
- (when (or (equal (plist-get plist ':type) "ref")
- (equal (plist-get plist ':type) "eqref")
- (equal (plist-get plist ':type) "pageref")
- (equal (plist-get plist ':type) "nameref"))
- (unless (-contains? labels (plist-get plist :path))
- (goto-char (plist-get plist :begin))
- (add-to-list
- 'bad-refs
- (cons (plist-get plist :path)
- (point-marker))))))))
- (goto-char cp)
- bad-refs))
-
-
-(defun org-ref-bad-label-candidates ()
- "Return a list of labels where label is multiply defined."
- (let ((labels (org-ref-get-labels))
- (multiple-labels '()))
- (when (not (= (length labels)
- (length (-uniq labels))))
- (dolist (label labels)
- (when (> (-count (lambda (a)
- (equal a label))
- labels) 1)
- ;; this is a multiply defined label.
- (let ((cp (point)))
- (goto-char (point-min))
- (while (re-search-forward
- (format "[^#+]label:%s\\s-" label) nil t)
- (push (cons label (point-marker)) multiple-labels))
-
- (goto-char (point-min))
- (while (re-search-forward
- (format "\\label{%s}\\s-?" label) nil t)
- (push (cons label (point-marker)) multiple-labels))
-
- (goto-char (point-min))
- (while (re-search-forward
- (format "^#\\+label:\\s-*%s" label) nil t)
- (push (cons label (point-marker)) multiple-labels))
-
- (goto-char (point-min))
- (while (re-search-forward
- (format "^#\\+tblname:\\s-*%s" label) nil t)
- (push (cons label (point-marker)) multiple-labels))
- (goto-char cp)))))
- multiple-labels))
-#+END_SRC
+- newglossaryentry :: define a term
+- gls :: a reference to a term
+- glspl :: plural reference to a term
+- Gsl :: capitalized reference to a term
+- Glspl :: capitalized plural reference to a term
-#+RESULTS:
-: org-ref-bad-label-candidates
-
-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
-(defun org-ref ()
- "Opens a helm interface to actions for org-ref.
-Shows bad citations, ref links and labels"
- (interactive)
- (let ((cb (current-buffer))
- (bad-citations (org-ref-bad-cite-candidates))
- (bad-refs (org-ref-bad-ref-candidates))
- (bad-labels (org-ref-bad-label-candidates)))
-
- (helm :sources `(((name . "Bad citations")
- (candidates . ,bad-citations)
- (action . (lambda (marker)
- (switch-to-buffer (marker-buffer marker))
- (goto-char marker))))
- ;;
- ((name . "Bad Labels")
- (candidates . ,bad-labels)
- (action . (lambda (marker)
- (switch-to-buffer (marker-buffer marker))
- (goto-char marker))))
- ;;
- ((name . "Bad ref links")
- (candidates . ,bad-refs)
- (action . (lambda (marker)
- (switch-to-buffer (marker-buffer marker))
- (goto-char marker))))
- ;;
- ((name . "Utilities")
- (candidates . (("Check buffer again" . org-ref)
- ("Insert citation" . helm-bibtex)
- ("Insert label link" . org-ref-helm-insert-label-link)
- ("Insert ref link" . org-ref-helm-insert-ref-link)
- ("List of figures" . org-ref-list-of-figures)
- ("List of tables" . org-ref-list-of-tables)
- ("Table of contents" . nil)
- ))
- (action . (lambda (x)
- (switch-to-buffer ,cb)
- (funcall x))))
- ;;
- ((name . "Export functions")
- (candidates . (("Extract cited entries" . org-ref-extract-bibtex-entries)
- ("Export to html and open" . (lambda () (org-open-file (org-html-export-to-html))))
- ("Export to pdf and open" . (lambda ()
- (org-open-file (org-latex-export-to-pdf))))
- ("Export to manuscript pdf and open" . ox-manuscript-export-and-build-and-open)
- ("Export submission manuscript pdf and open" . ox-manuscript-build-submission-manuscript-and-open)
-
- ))
- (action . (lambda (x)
- (switch-to-buffer ,cb)
- (funcall x))))
- ))))
-#+END_SRC
+You will need to incorporate running the command makeglossaries into your PDF build command. You also need use the glossaries LaTeX package.
+#+BEGIN_EXAMPLE
+#+LATEX_HEADER: \usepackage[toc]{glossaries}
+#+END_EXAMPLE
-** Finding non-ascii characters
-I like my bibtex files to be 100% ascii. This function finds the non-ascii characters so you can replace them.
+This is not supported in anything but LaTeX export.
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-find-non-ascii-characters ()
- "finds non-ascii characters in the buffer. Useful for cleaning up bibtex files"
- (interactive)
- (occur "[^[:ascii:]]"))
-#+END_SRC
+* Index
+This is a functional link that will open a buffer of clickable index entries:
+printindex:nil
-** Resort a bibtex entry
-I like neat and orderly bibtex entries.That means the fields are in a standard order that I like. This function reorders the fields in an entry for articles, and makes sure the fields are in lowercase.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-sort-bibtex-entry ()
- "sort fields of entry in standard order and downcase them"
- (interactive)
- (bibtex-beginning-of-entry)
- (let* ((master '("author" "title" "journal" "volume" "number" "pages" "year" "doi" "url"))
- (entry (bibtex-parse-entry))
- (entry-fields)
- (other-fields)
- (type (cdr (assoc "=type=" entry)))
- (key (cdr (assoc "=key=" entry))))
-
- ;; these are the fields we want to order that are in this entry
- (setq entry-fields (mapcar (lambda (x) (car x)) entry))
- ;; we do not want to reenter these fields
- (setq entry-fields (remove "=key=" entry-fields))
- (setq entry-fields (remove "=type=" entry-fields))
-
- ;;these are the other fields in the entry
- (setq other-fields (remove-if-not (lambda(x) (not (member x master))) entry-fields))
-
- (cond
- ;; right now we only resort articles
- ((string= (downcase type) "article")
- (bibtex-kill-entry)
- (insert
- (concat "@article{" key ",\n"
- (mapconcat
- (lambda (field)
- (when (member field entry-fields)
- (format "%s = %s," (downcase field) (cdr (assoc field entry))))) master "\n")
- (mapconcat
- (lambda (field)
- (format "%s = %s," (downcase field) (cdr (assoc field entry)))) other-fields "\n")
- "\n}\n\n"))
- (bibtex-find-entry key)
- (bibtex-fill-entry)
- (bibtex-clean-entry)
- ))))
-#+END_SRC
+* Other forms of this document
+** PDF
+You may want to build a pdf of this file. Here is an emacs-lisp block that will create and open the PDF.
-** Clean a bibtex entry
- I like neat and orderly bibtex entries. This code will eventually replace the key with my style key, clean the entry, and sort the fields in the order I like them.
-see [[file:emacs-24.3/lisp/textmodes/bibtex.el::bibtex-autokey-before-presentation-function]] for how to set a function that checks for uniqueness of the key.
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-clean-bibtex-entry(&optional keep-key)
- "clean and replace the key in a bibtex function. When keep-key is t, do not replace it. You can use a prefix to specify the key should be kept"
- (interactive "P")
- (bibtex-beginning-of-entry)
-(end-of-line)
- ;; some entries do not have a key or comma in first line. We check and add it, if needed.
- (unless (string-match ",$" (thing-at-point 'line))
- (end-of-line)
- (insert ","))
-
- ;; check for empty pages, and put eid or article id in its place
- (let ((entry (bibtex-parse-entry))
- (pages (bibtex-autokey-get-field "pages"))
- (year (bibtex-autokey-get-field "year"))
- (doi (bibtex-autokey-get-field "doi"))
- ;; The Journal of Chemical Physics uses eid
- (eid (bibtex-autokey-get-field "eid")))
-
- ;; replace http://dx.doi.org/ in doi. some journals put that in,
- ;; but we only want the doi.
- (when (string-match "^http://dx.doi.org/" doi)
- (bibtex-beginning-of-entry)
- (goto-char (car (cdr (bibtex-search-forward-field "doi" t))))
- (bibtex-kill-field)
- (bibtex-make-field "doi")
- (backward-char)
- (insert (replace-regexp-in-string "^http://dx.doi.org/" "" doi)))
-
- ;; asap articles often set year to 0, which messes up key
- ;; generation. fix that.
- (when (string= "0" year)
- (bibtex-beginning-of-entry)
- (goto-char (car (cdr (bibtex-search-forward-field "year" t))))
- (bibtex-kill-field)
- (bibtex-make-field "year")
- (backward-char)
- (insert (read-string "Enter year: ")))
-
- ;; fix pages if they are empty if there is an eid to put there.
- (when (string= "-" pages)
- (when eid
- (bibtex-beginning-of-entry)
- ;; this seems like a clunky way to set the pages field.But I
- ;; cannot find a better way.
- (goto-char (car (cdr (bibtex-search-forward-field "pages" t))))
- (bibtex-kill-field)
- (bibtex-make-field "pages")
- (backward-char)
- (insert eid)))
-
- ;; replace naked & with \&
- (save-restriction
- (bibtex-narrow-to-entry)
- (bibtex-beginning-of-entry)
- (message "checking &")
- (replace-regexp " & " " \\\\& ")
- (widen))
-
- ;; generate a key, and if it duplicates an existing key, edit it.
- (unless keep-key
- (let ((key (bibtex-generate-autokey)))
-
- ;; first we delete the existing key
- (bibtex-beginning-of-entry)
- (re-search-forward bibtex-entry-maybe-empty-head)
- (if (match-beginning bibtex-key-in-head)
- (delete-region (match-beginning bibtex-key-in-head)
- (match-end bibtex-key-in-head)))
- ;; check if the key is in the buffer
- (when (save-excursion
- (bibtex-search-entry key))
- (save-excursion
- (bibtex-search-entry key)
- (bibtex-copy-entry-as-kill)
- (switch-to-buffer-other-window "*duplicate entry*")
- (bibtex-yank))
- (setq key (bibtex-read-key "Duplicate Key found, edit: " key)))
-
- (insert key)
- (kill-new key))) ;; save key for pasting
-
- ;; run hooks. each of these operates on the entry with no arguments.
- ;; this did not work like i thought, it gives a symbolp error.
- ;; (run-hooks org-ref-clean-bibtex-entry-hook)
- (mapcar (lambda (x)
- (save-restriction
- (save-excursion
- (funcall x))))
- org-ref-clean-bibtex-entry-hook)
-
- ;; sort fields within entry
- (org-ref-sort-bibtex-entry)
- ;; check for non-ascii characters
- (occur "[^[:ascii:]]")
- ))
+#+BEGIN_SRC emacs-lisp
+(org-open-file (org-latex-export-to-pdf))
#+END_SRC
#+RESULTS:
-: org-ref-clean-bibtex-entry
-
-** Sort the entries in a citation link by year
-I prefer citations in chronological order within a grouping. These functions sort the link under the cursor by year.
-
-#+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
- (insert-file-contents bibfile)
- (bibtex-search-entry key nil 0)
- (prog1 (reftex-get-bib-field "year" (bibtex-parse-entry t))
- ))))
-
-(defun org-ref-sort-citation-link ()
- "replace link at point with sorted link by year"
- (interactive)
- (let* ((object (org-element-context))
- (type (org-element-property :type object))
- (begin (org-element-property :begin object))
- (end (org-element-property :end object))
- (link-string (org-element-property :path object))
- keys years data)
- (setq keys (org-ref-split-and-strip-string link-string))
- (setq years (mapcar 'org-ref-get-citation-year keys))
- (setq data (mapcar* (lambda (a b) `(,a . ,b)) years keys))
- (setq data (cl-sort data (lambda (x y) (< (string-to-int (car x)) (string-to-int (car y))))))
- ;; now get the keys separated by commas
- (setq keys (mapconcat (lambda (x) (cdr x)) data ","))
- ;; and replace the link with the sorted keys
- (cl--set-buffer-substring begin end (concat type ":" keys))))
-#+END_SRC
-** Sort entries in citation links with shift-arrow keys
-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"
- (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)
- (let* ((object (org-element-context))
- (type (org-element-property :type object))
- (begin (org-element-property :begin object))
- (end (org-element-property :end object))
- (link-string (org-element-property :path object))
- key keys i)
- ;; We only want this to work on citation links
- (when (-contains? org-ref-cite-types type)
- (setq key (org-ref-get-bibtex-key-under-cursor))
- (setq keys (org-ref-split-and-strip-string link-string))
- (setq i (index key keys)) ;; defined in org-ref
- (if (> direction 0) ;; shift right
- (org-ref-swap-keys i (+ i 1) keys)
- (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 " "))
- ;; now go forward to key so we can move with the key
- (re-search-forward key)
- (goto-char (match-beginning 0)))))
-
-;; add hooks to make it work
-(add-hook 'org-shiftright-hook (lambda () (org-ref-swap-citation-link 1)))
-(add-hook 'org-shiftleft-hook (lambda () (org-ref-swap-citation-link -1)))
-#+END_SRC
+** HTML
+You may want to build an html version of this file. Here is an emacs-lisp block that will create and open the html in your browser. You will see the bibliography is not perfect, but it is pretty functional.
-** Lightweight messages about links
-To get a lighter weight message about the label, ref and cite links, we define a function that gives us the minibuffer message, without the menu. We run this in an idle timer.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun org-ref-get-label-context (label)
- "Return a string of context around a label."
- (save-excursion
- (catch 'result
- (goto-char (point-min))
- (when (re-search-forward
- (format "label:%s\\b" label) nil t)
- (throw 'result (buffer-substring
- (progn
- (previous-line)
- (beginning-of-line)
- (point))
- (progn
- (forward-line 4)
- (point)))))
-
- (goto-char (point-min))
- (when (re-search-forward
- (format "\\label{%s}" label) nil t)
- (throw 'result (buffer-substring
- (progn
- (previous-line)
- (beginning-of-line)
- (point))
- (progn
- (forward-line 4)
- (point)))))
-
- (goto-char (point-min))
- (when (re-search-forward
- (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t)
- (throw 'result (buffer-substring
- (progn
- (previous-line)
- (beginning-of-line)
- (point))
- (progn
- (forward-line 4)
- (point)))))
-
- (goto-char (point-min))
- (when (re-search-forward
- (format "^#\\+tblname:\\s-*\\(%s\\)\\b" label) nil t)
- (throw 'result (buffer-substring
- (progn
- (previous-line)
- (beginning-of-line)
- (point))
- (progn
- (forward-line 4)
- (point)))))
- (throw 'result "!!! NO CONTEXT FOUND !!!"))))
-
-
-(defun org-ref-link-message ()
- "Print a minibuffer message about the link that point is on."
- (interactive)
- (when (eq major-mode 'org-mode)
- (let* ((object (org-element-context))
- (type (org-element-property :type object)))
- (save-excursion
- (cond
- ;; cite links
- ((-contains? org-ref-cite-types type)
- (message (org-ref-get-citation-string-at-point)))
-
- ;; message some context about the label we are referring to
- ((string= type "ref")
- (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 "%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
- (message (concat
- (number-to-string count)
- " occurence"
- (when (or (= count 0)
- (> count 1))
- "s")))))
-
- ((string= type "custom-id")
- (save-excursion
- (org-open-link-from-string
- (format "[[#%s]]" (org-element-property :path object)))
- (message "%s" (org-get-heading))))
-
- ;; check if the bibliography files exist.
- ((string= type "bibliography")
- (let* ((bibfile)
- ;; object is the link you clicked on
- (object (org-element-context))
- (link-string (org-element-property :path object))
- (link-string-beginning)
- (link-string-end))
- (save-excursion
- (goto-char (org-element-property :begin object))
- (search-forward link-string nil nil 1)
- (setq link-string-beginning (match-beginning 0))
- (setq link-string-end (match-end 0)))
-
- ;; make sure we are in link and not before the :
- (when (> link-string-beginning (point))
- (goto-char link-string-beginning))
-
- ;; now if we have comma separated bibliographies
- ;; we find the one clicked on. we want to
- ;; search forward to next comma from point
- (save-excursion
- (if (search-forward "," link-string-end 1 1)
- (setq key-end (- (match-end 0) 1)) ; we found a match
- (setq key-end (point)))) ; no comma found so take the point
-
- ;; and backward to previous comma from point
- (save-excursion
- (if (search-backward "," link-string-beginning 1 1)
- (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
- (setq key-beginning (point)))) ; no match found
- ;; save the key we clicked on.
- (setq bibfile
- (org-ref-strip-string
- (buffer-substring key-beginning key-end)))
- (if (file-exists-p bibfile)
- (message "%s exists." bibfile)
- (message "!!! %s NOT FOUND !!!" bibfile))))
- )))))
-#+END_SRC
-
-* Aliases
-I like convenience. Here are some aliases for faster typing.
-
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defalias 'oro 'org-ref-open-citation-at-point)
-(defalias 'orc 'org-ref-citation-at-point)
-(defalias 'orp 'org-ref-open-pdf-at-point)
-(defalias 'oru 'org-ref-open-url-at-point)
-(defalias 'orn 'org-ref-open-notes-at-point)
-(defalias 'ornr 'org-ref-open-notes-from-reftex)
-
-(defalias 'orib 'org-ref-insert-bibliography-link)
-(defalias 'oric 'org-ref-insert-cite-link)
-(defalias 'orir 'org-ref-insert-ref-link)
-(defalias 'orsl 'org-ref-store-bibtex-entry-link)
-
-(defalias 'orcb 'org-ref-clean-bibtex-entry)
-#+END_SRC
-* 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.
-
-1. Make the default action to insert selected keys.
-2. Make open entry second action
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(setq helm-source-bibtex
- '((name . "BibTeX entries")
- (init . helm-bibtex-init)
- (candidates . helm-bibtex-candidates)
- (filtered-candidate-transformer . helm-bibtex-candidates-formatter)
- (action . (("Insert citation" . helm-bibtex-insert-citation)
- ("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 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)
- ))))
-#+END_SRC
-
-Now, let us define a function that inserts the cite links:
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(defun helm-bibtex-format-org-ref (keys)
- "Insert selected KEYS as cite link. Append KEYS if you are on a link.
-Technically, this function should return a string that is inserted by helm. This function does the insertion and gives helm an empty string to insert. This lets us handle appending to a link properly.
-
-In the helm-bibtex buffer, C-u will give you a helm menu to select a new link type for the selected entries.
-
-C-u C-u will change the key at point to the selected keys.
-"
- (let* ((object (org-element-context))
- (last-char (save-excursion
- (goto-char (org-element-property :end object))
- (backward-char)
- (if (looking-at " ")
- " "
- ""))))
- (cond
- ;; case where we are in a link
- ((and (equal (org-element-type object) 'link)
- (-contains?
- org-ref-cite-types
- (org-element-property :type object)))
- (cond
- ;; no prefix. append keys
- ((equal helm-current-prefix-arg nil)
- (goto-char (org-element-property :end object))
- (while (looking-back " ") (backward-char))
- (insert (concat "," (mapconcat 'identity keys ","))))
- ;; double prefix, replace key at point
- ((equal helm-current-prefix-arg '(16))
- (setf (buffer-substring
- (org-element-property :begin object)
- (org-element-property :end object))
- (concat
- (replace-regexp-in-string
- (car (org-ref-get-bibtex-key-and-file)) ; key
- (mapconcat 'identity keys ",") ; new keys
- (org-element-property :raw-link object))
- ;; replace space at end to avoid collapsing into next word.
- 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"))))
-
- ;; We are next to a link, and we want to append
- ;; next to a link means one character back is on a link.
- ((save-excursion
- (backward-char)
- (and (equal (org-element-type (org-element-context)) 'link)
- (-contains?
- org-ref-cite-types
- (org-element-property :type (org-element-context)))))
- (while (looking-back " ") (backward-char))
- (insert (concat "," (mapconcat 'identity keys ","))))
-
- ;; insert fresh link
- (t
- ;;(message-box "fresh link")
- (insert
- (concat (if (equal helm-current-prefix-arg '(4))
- (helm :sources `((name . "link types")
- (candidates . ,org-ref-cite-types)
- (action . (lambda (x) x))))
- org-ref-default-citation-link)
- ":"
- (s-join "," keys))))))
- ;; return empty string for helm
- "")
-
-(setq helm-bibtex-format-citation-functions
- '((org-mode . helm-bibtex-format-org-ref)))
-
-(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.
-With two prefix args, insert a label link."
- (interactive "P")
- (cond
- ((equal arg nil)
- (let ((helm-bibtex-bibliography (org-ref-find-bibliography)))
- (helm-bibtex)))
- ((equal arg '(4))
- (org-ref-helm-insert-ref-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
- (-insert-at 1 '("Crossref" . "http://search.crossref.org/?q=%s") helm-bibtex-fallback-options))
-
-(setq helm-bibtex-fallback-options
- (-insert-at
- 1
- '("Scopus" . "http://www.scopus.com/scopus/search/submit/xadvanced.url?searchfield=TITLE-ABS-KEY(%s)")
- helm-bibtex-fallback-options))
-
-(setq 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
-This code provides a helm interface to things you can do when you click on a citation link. This is an alternative to the minibuffer menu.
-#+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)))
- (if bibfile
- (save-excursion
- (with-temp-buffer
- (insert-file-contents bibfile)
- (bibtex-search-entry key)
- (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))
- (bibfile (cdr results))
- (url (save-excursion
- (with-temp-buffer
- (insert-file-contents bibfile)
- (bibtex-search-entry key)
- (bibtex-autokey-get-field "url"))))
- (doi (save-excursion
- (with-temp-buffer
- (insert-file-contents bibfile)
- (bibtex-search-entry key)
- ;; I like this better than bibtex-url which does not always find
- ;; the urls
- (bibtex-autokey-get-field "doi"))))
- (candidates `(("Quit" . org-ref-citation-at-point)
- ("Open bibtex entry" . org-ref-open-citation-at-point))))
- ;; for some reason, when there is no doi or url, they are returned as "". I
- ;; prefer nil so we correct this here.
- (when (string= doi "") (setq doi nil))
- (when (string= url "") (setq url nil))
-
- ;; Conditional pdf functions
- (if (file-exists-p pdf-file)
- (add-to-list
- 'candidates
- '("Open pdf" . org-ref-open-pdf-at-point)
- t)
- (add-to-list
- 'candidates
- '("Try to get pdf" . (lambda ()
- (save-window-excursion
- (org-ref-open-citation-at-point)
- (bibtex-beginning-of-entry)
- (doi-utils-get-bibtex-entry-pdf))))
- t))
-
-
- (add-to-list
- 'candidates
- '("Open notes" . org-ref-open-notes-at-point)
- t)
-
- ;; conditional url and doi functions
- (when (or url doi)
- (add-to-list
- 'candidates
- '("Open in browser" . org-ref-open-url-at-point)
- t))
-
- (when doi
- (mapc (lambda (x)
- (add-to-list 'candidates x t))
- `(("WOS" . org-ref-wos-at-point)
- ("Related articles in WOS" . org-ref-wos-related-at-point)
- ("Citing articles in WOS" . org-ref-wos-citing-at-point)
- ("Google Scholar" . org-ref-google-scholar-at-point)
- ("Pubmed" . org-ref-pubmed-at-point)
- ("Crossref" . org-ref-crossref-at-point)
- )))
-
- (add-to-list
- 'candidates
- '("Copy formatted citation to clipboard" . org-ref-copy-entry-as-summary)
- t)
-
- (add-to-list
- 'candidates
- '("Copy key to clipboard" . (lambda ()
- (kill-new
- (car (org-ref-get-bibtex-key-and-file)))))
- t)
-
- (add-to-list
- 'candidates
- '("Copy bibtex entry to file" . org-ref-copy-entry-at-point-to-file)
- t)
-
- (add-to-list
- 'candidates
- '("Email bibtex entry and pdf" . (lambda ()
- (save-excursion
- (org-ref-open-citation-at-point)
- (email-bibtex-entry))))
- t)
- ;; finally return a numbered list of the candidates
- (loop for i from 0
- for cell in candidates
- collect (cons (format "%2s. %s" i (car cell))
- (cdr cell)))))
-
-
-(defvar org-ref-helm-user-candidates '()
- "List of user-defined candidates to act when clicking on a cite link.
-This is a list of cons cells '((\"description\" . action)). The action function should not take an argument, and should assume point is on the cite key of interest.
-")
-
-;; example of adding your own function
-(add-to-list
- 'org-ref-helm-user-candidates
- '("Example" . (lambda () (message-box "You did it!")))
- t)
-
-(defun org-ref-cite-click-helm (key)
- "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)
- (let ((name (org-ref-get-citation-string-at-point))
- (candidates (org-ref-cite-candidates))
- (cb (current-buffer)))
-
- (helm :sources `(((name . ,name)
- (candidates . ,candidates)
- (action . (lambda (f)
- (switch-to-buffer cb)
- (funcall f))))
- ((name . "User functions")
- (candidates . ,org-ref-helm-user-candidates)
- (action . (lambda (f)
- (switch-to-buffer cb)
- (funcall f))))
- ))))
+#+BEGIN_SRC emacs-lisp
+(browse-url (org-html-export-to-html))
#+END_SRC
#+RESULTS:
-: org-ref-cite-click-helm
-
-* End of code
-#+BEGIN_SRC emacs-lisp :tangle org-ref.el
-(provide 'org-ref)
-#+END_SRC
-
-* Build :noexport:
-This code will tangle the elisp code out to org-ref.el and load it.
-
-[[elisp:(progn (org-babel-tangle) (load-file "org-ref.el"))]]
-
-Alternatively you may use:
+: #<process open ./org-ref.html>
-[[elisp:(org-babel-load-file "org-ref.org")]]
+* References
+bibliographystyle:unsrtnat
+# <<bibliography link>>
+bibliography:org-ref.bib
projects / org-ref.git / blobdiff