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1380 lines
49 KiB
1380 lines
49 KiB
;;; org-ref-bibtex.el -- org-ref-bibtex utilities
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;; Copyright(C) 2014 John Kitchin
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;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
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;; URL: https://github.com/jkitchin/org-ref
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;; Version: 0.1
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;; Keywords: org-mode, bibtex
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;; Package-Requires: ((org-ref) (s) (dash) (doi-utils) (key-chord))
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;; This file is not currently part of GNU Emacs.
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;; This program is free software; you can redistribute it and/or
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;; modify it under the terms of the GNU General Public License as
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;; published by the Free Software Foundation; either version 2, or (at
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;; your option) any later version.
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;; This program is distributed in the hope that it will be useful, but
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;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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;; General Public License for more details.
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;; You should have received a copy of the GNU General Public License
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;; along with this program ; see the file COPYING. If not, write to
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;; the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
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;; Boston, MA 02111-1307, USA.
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;;; Commentary:
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;; org-ref-bibtex-generate-longtitles
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;; org-ref-bibtex-generate-shorttitles
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;; org-ref-stringify-journal-name :: replace a journal name with a string in
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;; `org-ref-bibtex-journal-abbreviations'
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;; org-ref-set-journal-string :: in a bibtex entry run this to replace the
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;; journal with a string
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;;
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;; org-ref-title-case-article :: title case the title in an article or book
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;; org-ref-sentence-case-article :: sentence case the title in an article.
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;; org-ref-replace-nonascii :: replace nonascii characters in a bibtex
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;; entry. Replacements are in `org-ref-nonascii-latex-replacements'.
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;;
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;; org-ref-title-case-article
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;; org-ref-sentence-case-article
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;;
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;; org-ref-bibtex-next-entry :: bound to M-n
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;; org-ref-bibtex-previous-entry :: bound to M-p
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;;
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;; Functions to act on a bibtex entry or file
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;; org-ref-bibtex-hydra/body gives a hydra menu to a lot of useful functions.
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;; org-ref-bibtex-new-entry/body gives a hydra menu to add new bibtex entries.
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;; org-ref-bibtex-file/body gives a hydra menu of actions for the bibtex file
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;;
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;; org-ref-bibtex :: a deprecated menu of actions
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(require 'bibtex)
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(require 'dash)
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(require 'hydra)
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(require 'key-chord nil 'no-error)
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(require 'message)
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(require 's)
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(require 'org-ref-citeproc)
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(require 'doi-utils)
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(defvar org-ref-pdf-directory)
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(defvar org-ref-notes-directory)
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(defvar org-ref-default-bibliography)
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(declare-function reftex-get-bib-field "reftex-cite")
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(declare-function key-chord-define-global "key-chord")
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(declare-function org-ref-find-bibliography "org-ref-core")
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(declare-function org-ref-open-bibtex-pdf "org-ref-core")
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(declare-function org-ref-open-bibtex-notes "org-ref-core")
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(declare-function org-ref-clean-bibtex-entry "org-ref-core")
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(declare-function org-ref-open-in-browser "org-ref-core")
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(declare-function org-ref-sort-bibtex-entry "org-ref-core")
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(declare-function org-ref-build-full-bibliography "org-ref-core")
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(declare-function helm-tag-bibtex-entry "org-ref-helm")
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(declare-function bibtex-completion-edit-notes "bibtex-completion")
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(declare-function bibtex-completion-get-value "bibtex-completion")
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(declare-function bibtex-completion-get-entry "bibtex-completion")
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(declare-function parsebib-find-next-item "parsebib")
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(declare-function parsebib-read-entry "parsebib")
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(declare-function helm-bibtex "helm-bibtex")
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(declare-function helm "helm")
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;;; Code:
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;; This is duplicated from org-ref-core to try to avoid a byte-compile error.
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(add-to-list 'load-path
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(expand-file-name
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"citeproc"
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(file-name-directory (or load-file-name (buffer-file-name)))))
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(add-to-list 'load-path
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(expand-file-name
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"citeproc/csl"
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(file-name-directory (or load-file-name (buffer-file-name)))))
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;;* Custom variables
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(defgroup org-ref-bibtex nil
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"Customization group for org-ref-bibtex."
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:group 'org-ref-bibtex)
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(defcustom org-ref-bibtex-hydra-key-chord
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nil
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"Key-chord to run `org-ref-bibtex-hydra'.
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I like \"jj\""
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:type '(choice (const nil :tag "None")
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(string))
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:group 'org-ref-bibtex)
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(defcustom org-ref-bibtex-hydra-key-binding
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nil
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"Key-binding to run `org-ref-bibtex-hydra'.
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I like \"C-c j\"."
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:type '(choice (const nil :tag "No binding")
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(key-sequence))
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:group 'org-ref-bibtex)
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(defcustom org-ref-helm-cite-shorten-authors nil
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"If non-nil show only last names in the helm selection buffer."
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:type 'boolean
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:group 'org-ref-bibtex)
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(defcustom org-ref-formatted-citation-formats
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'(("text" . (("article" . "${author}, ${title}, ${journal}, ${volume}(${number}), ${pages} (${year}). ${doi}")
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("inproceedings" . "${author}, ${title}, In ${editor}, ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
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("book" . "${author}, ${title} (${year}), ${address}: ${publisher}.")
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("phdthesis" . "${author}, ${title} (Doctoral dissertation) (${year}). ${school}, ${address}.")
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("inbook" . "${author}, ${title}, In ${editor} (Eds.), ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
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("incollection" . "${author}, ${title}, In ${editor} (Eds.), ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
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("proceedings" . "${editor} (Eds.), ${booktitle} (${year}). ${address}: ${publisher}.")
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("unpublished" . "${author}, ${title} (${year}). Unpublished manuscript.")
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(nil . "${author}, ${title} (${year}).")))
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("org" . (("article" . "${author}, /${title}/, ${journal}, *${volume}(${number})*, ${pages} (${year}). ${doi}")
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("inproceedings" . "${author}, /${title}/, In ${editor}, ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
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("book" . "${author}, /${title}/ (${year}), ${address}: ${publisher}.")
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("phdthesis" . "${author}, /${title}/ (Doctoral dissertation) (${year}). ${school}, ${address}.")
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("inbook" . "${author}, /${title}/, In ${editor} (Eds.), ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
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("incollection" . "${author}, /${title}/, In ${editor} (Eds.), ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
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("proceedings" . "${editor} (Eds.), _${booktitle}_ (${year}). ${address}: ${publisher}.")
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("unpublished" . "${author}, /${title}/ (${year}). Unpublished manuscript.")
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(nil . "${author}, /${title}/ (${year})."))))
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"Format strings for formatted bibtex entries for different citation backends.
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Used in `org-ref-format-entry'."
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:type '(alist)
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:group 'org-ref-bibtex)
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(defcustom org-ref-formatted-citation-backend "text"
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"The backend format for formatted citations.
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Should be one of the cars of `org-ref-formatted-citation-formats'."
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:type 'string
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:group 'org-ref-bibtex)
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;;* Journal abbreviations
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(defvar org-ref-bibtex-journal-abbreviations
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'()
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"List of (string journal-full-name journal-abbreviation). Find
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new abbreviations at http://cassi.cas.org/search.jsp.")
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(defcustom org-ref-bibtex-assoc-pdf-with-entry-move-function 'rename-file
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"Function to use when associating pdf files with bibtex entries.
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The value should be either `rename-file' or `copy-file'. The former
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will move and rename the original file. The latter will leave the
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original file in place while creating a renamed copy in
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`org-ref-pdf-directory'."
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:type 'function
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:group 'org-ref-bibtex)
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(setq org-ref-bibtex-journal-abbreviations
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'(("ACR" "Accounts of Chemical Research" "Acc. Chem. Res.")
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("ACAT" "ACS Catalysis" "ACS Catal.")
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("AM" "Acta Materialia" "Acta Mater.")
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("AMM" "Acta Metallurgica et Materialia" "Acta Metall. Mater.")
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("AEM" "Advanced Energy Materials" "Adv. Energy Mater.")
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("AAMI" "ACS Applied Materials \\& Interfaces"
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"ACS Appl. Mater. Interfaces")
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("AMiner" "American Mineralogist" "Am. Mineral.")
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("AngC" "Angewandte Chemie-International Edition"
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"Angew. Chem. Int. Edit.")
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("APLM" "APL Materials" "APL Mat.")
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("ACBE" "Applied Catalysis B: Environmental" "Appl. Catal. B-Environ.")
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("APL" "Applied Physics Letters" "Appl. Phys. Lett.")
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("ASS" "Applied Surface Science" "Appl. Surf. Sci.")
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("CL" "Catalysis Letters" "Catal. Lett.")
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("CC" "Catalysis Communications" "Catal. Commun.")
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("CST" "Catalysis Science & Technology" "Catal. Sci. Technol.")
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("CT" "Catalysis Today" "Catal. Today")
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("ChC" "Chemical Communications" "Chem. Commun.")
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("CPL" "Chemical Physics Letters" "Chem. Phys. Lett")
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("CR" "Chemical Reviews" "Chem. Rev.")
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("CSR" "Chemical Society Reviews" "Chem. Soc. Rev.")
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("CSR" "Chemical Society Reviews" "Chem. Soc. Rev.")
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("CM" "Chemistry of Materials" "Chem. Mater.")
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("CSA" "Colloids and Surfaces, A: Physicochemical and Engineering Aspects"
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"Colloids Surf., A")
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("CF" "Combustion and Flame" "Combust. Flame")
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("CPMS" "Computational Materials Science" "Comp. Mater. Sci.")
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("CPC" "Computer Physics Communications" "Comput. Phys. Commun.")
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("CSE" "Computing in Science \\& Engineering" "Comput. Sci. Eng.")
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("CGD" "Crystal Growth \\& Design" "Cryst. Growth Des.")
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("CEC" "CrystEngComm" "CrystEngComm")
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("EA" "Electrochimica Acta" "Electrochim. Acta")
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("ECST" "ECS Transactions" "ECS Trans.")
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("EES" "Energy \\& Environmental Science" "Energy Environ. Sci.")
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("HPR" "High Pressure Research" "High Pressure Res.")
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("IC" "Inorganic Chemistry" "Inorg. Chem.")
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("IECR" "Industrial \\& Engineering Chemistry Research"
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"Ind. Eng. Chem. Res.")
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("JJAP" "Japanese Journal of Applied Physics" "Jpn. J. Appl. Phys.")
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("JMatR" "Journal of Materials Research" "J. Mater. Res.")
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("JALC" "Journal of Alloys and Compounds" "J. Alloy Compd.")
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("JAC" "Journal of Applied Crystallography" "J. Appl. Crystallogr.")
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("JAE" "Journal of Applied Electrochemistry" "J. Appl. Electrochem.")
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("JAP" "Journal of Applied Physics" "J. Appl. Phys.")
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("JC" "Journal of Catalysis" "J. Catal.")
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("JCP" "Journal of Chemical Physics" "J. Chem. Phys.")
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("JCC" "Journal of Computational Chemistry" "J. Comput. Chem.")
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("JCG" "Journal of Crystal Growth" "J. Crys. Growth")
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("JMC" "Journal of Materials Chemistry" "J. Mater. Chem.")
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("JMC" "Journal of Materials Chemistry" "J. Mater. Chem.")
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("JMSL" "Journal of Materials Science Letters" "J. Mater. Sci. Lett.")
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("JMS" "Journal of Membrane Science" "J. Memb. Sci.")
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("JPE" "Journal of Phase Equilibria" "J. Phase Equilib.")
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("JPCS" "Journal of Physics and Chemistry of Solids"
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"J. Phys. Chem. Solids")
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("JPCM" "Journal of Physics: Condensed Matter"
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"J. Phys.: Condens. Matter")
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("JPS" "Journal of Power Sources" "J. Power Sources")
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("JSSC" "Journal of Solid State Chemistry" "J. Solid State Chem.")
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("JACerS" "Journal of the American Ceramic Society" "J. Am. Ceram. Soc.")
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("JACS" "Journal of the American Chemical Society" "J. Am. Chem. Soc.")
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("JASIST" "Journal of the American Society for Information Science and Technology"
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"J. Am. Soc. Inf. Sci. Technol.")
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("JES" "Journal of The Electrochemical Society" "J. Electrochem. Soc.")
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("JEaC" "Journal of Electroanalytical Chemistry" "J. Electroanal. Chem.")
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("JMS" "Journal of Membrane Science" "J. Memb. Sci.")
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("JRS" "Journal of Raman Spectroscopy" "J. Raman Spectrosc.")
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("JVST" "Journal of Vacuum Science \\& Technology A"
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"J. Vac. Sci. Technol. A")
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("ML" "Materials Letters" "Mater. Lett.")
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("MSE-BS" "Materials Science and Engineering B" "Mat. Sci. Eng. B-Solid")
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("MOLSIM" "Molecular Simulation" "Mol. Sim.")
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("Nature" "Nature" "Nature")
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("NM" "Nature Materials" "Nat. Mater.")
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("NC" "Nature Chemistry" "Nat. Chem.")
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("PML" "Philosophical Magazine Letters" "Phil. Mag. Lett.")
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("PMA" "Philosophical Magazine A" "Phil. Mag. A")
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("PA" "Physica A: Statistical Mechanics and its Applications" "Physica A")
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("PB" "Physica B-Condensed Matter" "Physica B")
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("PCCP" "Physical Chemistry Chemical Physics" "Phys. Chem. Chem. Phys.")
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("PSSB" "physica status solidi (b)" "Phys. Status Solidi B")
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("PRA" "Physical Review A" "Phys. Rev. A")
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("PRB" "Physical Review B" "Phys. Rev. B")
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("PRL" "Physical Review Letters" "Phys. Rev. Lett.")
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("PCM" "Physics and Chemistry of Minerals" "Phys. Chem. Miner.")
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("PNAS" "Proceedings of the National Academy of Sciences of the United States of America"
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"Proc. Natl. Acad. Sci. U. S. A.")
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("PSurfSci" "Progress in Surface Science" "Prog. Surf. Sci.")
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("Science" "Science" "Science")
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("SM" "Scripta Materialia" "Scr. Mater.")
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("SABC" "Sensors and Actuators B: Chemical" "Sensor. Actuat. B-Chem.")
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("SS" "Surface Science" "Surf. Sci.")
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("EPJB" "The European Physical Journal B" "Eur. Phys. J. B")
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("JPC" "The Journal of Physical Chemistry" "J. Phys. Chem.")
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("JPCB" "The Journal of Physical Chemistry B" "J. Phys. Chem. B")
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("JPCC" "The Journal of Physical Chemistry C" "J. Phys. Chem. C")
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("JPCL" "The Journal of Physical Chemistry Letters"
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"J. Phys. Chem. Lett.")
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("JCP" "The Journal of Chemical Physics" "J. Chem. Phys.")
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("MSMSE" "Modelling and Simulation in Materials Science and Engineering"
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"Modell. Simul. Mater. Sci. Eng.")
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("TSF" "Thin Solid Films" "Thin Solid Films")
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("TC" "Topics in Catalysis" "Top. Catal.")
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("WR" "Water Research" "Water Res.")))
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;;;###autoload
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(defun org-ref-bibtex-generate-longtitles ()
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"Generate longtitles.bib which are @string definitions.
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The full journal names are in `org-ref-bibtex-journal-abbreviations'."
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(interactive)
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(with-temp-file "longtitles.bib"
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(dolist (row org-ref-bibtex-journal-abbreviations)
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(insert (format "@string{%s=\"%s\"}\n"
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(nth 0 row)
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(nth 1 row))))))
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;;;###autoload
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(defun org-ref-bibtex-generate-shorttitles ()
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"Generate shorttitles.bib which are @string definitions.
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The abbreviated journal names in `org-ref-bibtex-journal-abbreviations'."
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(interactive)
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(with-temp-file "shorttitles.bib"
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(dolist (row org-ref-bibtex-journal-abbreviations)
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(insert (format "@string{%s=\"%s\"}\n"
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(nth 0 row)
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(nth 2 row))))))
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;;;###autoload
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(defun org-ref-stringify-journal-name (&optional key start end)
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"Replace journal name in a bibtex entry with a string.
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The strings are defined in
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`org-ref-bibtex-journal-abbreviations'. The optional arguments KEY,
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START and END allow you to use this with `bibtex-map-entries'"
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(interactive)
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(bibtex-beginning-of-entry)
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(when
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(string= "article"
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(downcase
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(cdr (assoc "=type=" (bibtex-parse-entry)))))
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(let* ((full-names (mapcar
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(lambda (row)
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(cons (nth 1 row) (nth 0 row)))
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org-ref-bibtex-journal-abbreviations))
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(abbrev-names (mapcar
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(lambda (row)
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(cons (nth 2 row) (nth 0 row)))
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org-ref-bibtex-journal-abbreviations))
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(journal (s-trim (bibtex-autokey-get-field "journal")))
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(bstring (or
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(cdr (assoc journal full-names))
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(cdr (assoc journal abbrev-names)))))
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(when bstring
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(bibtex-set-field "journal" bstring t)
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(bibtex-fill-entry)))))
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;;;###autoload
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(defun org-ref-helm-set-journal-string ()
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"Helm interface to set a journal string in a bibtex entry.
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Entries come from `org-ref-bibtex-journal-abbreviations'."
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(interactive)
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(bibtex-set-field
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"journal"
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(helm :sources
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`((name . "journal")
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(candidates . ,(mapcar
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(lambda (x)
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(cons (format "%s | %s" (nth 1 x) (nth 2 x))
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(car x)))
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org-ref-bibtex-journal-abbreviations))
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(action . (lambda (x) (identity x))))
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:input (s-trim (bibtex-autokey-get-field "journal")))
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t)
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(bibtex-fill-entry)
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(bibtex-clean-entry))
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;;;###autoload
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(defun org-ref-set-journal-string (full-journal-name)
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"Set a bibtex journal name to the string that represents FULL-JOURNAL-NAME.
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This is defined in `org-ref-bibtex-journal-abbreviations'."
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(interactive (list
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(completing-read
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"Journal: "
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(mapcar
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(lambda (x)
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(nth 1 x))
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org-ref-bibtex-journal-abbreviations))))
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;; construct data alist for the string lookup.
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(let ((alist (mapcar
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(lambda (x)
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(cons (nth 1 x) (nth 0 x)))
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org-ref-bibtex-journal-abbreviations)))
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(bibtex-set-field "journal" (cdr (assoc full-journal-name alist)) t)
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(bibtex-fill-entry)
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(bibtex-clean-entry)))
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;;* Non-ascii character replacement
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;; see https://github.com/fxcoudert/tools/blob/master/doi2bib for more replacements
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(defvar org-ref-nonascii-latex-replacements
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'()
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"Cons list of non-ascii characters and their LaTeX representations.")
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(setq org-ref-nonascii-latex-replacements
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'(("í" . "{\\\\'i}")
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("æ" . "{\\\\ae}")
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("ć" . "{\\\\'c}")
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("é" . "{\\\\'e}")
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("ä" . "{\\\\\"a}")
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("è" . "{\\\\`e}")
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("à" . "{\\\\`a}")
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("á" . "{\\\\'a}")
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("ø" . "{\\\\o}")
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("ë" . "{\\\\\"e}")
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("ü" . "{\\\\\"u}")
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("ñ" . "{\\\\~n}")
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("ņ" . "{\\\\c{n}}")
|
|
("ñ" . "{\\\\~n}")
|
|
("å" . "{\\\\aa}")
|
|
("ö" . "{\\\\\"o}")
|
|
("Á" . "{\\\\'A}")
|
|
("í" . "{\\\\'i}")
|
|
("ó" . "{\\\\'o}")
|
|
("ó" . "{\\\\'o}")
|
|
("ú" . "{\\\\'u}")
|
|
("ú" . "{\\\\'u}")
|
|
("ý" . "{\\\\'y}")
|
|
("š" . "{\\\\v{s}}")
|
|
("č" . "{\\\\v{c}}")
|
|
("ř" . "{\\\\v{r}}")
|
|
("š" . "{\\\\v{s}}")
|
|
("İ" . "{\\\\.I}")
|
|
("ğ" . "{\\\\u{g}}")
|
|
("δ" . "$\\\\delta$")
|
|
("ç" . "{\\\\c{c}}")
|
|
("ß" . "{\\\\ss}")
|
|
("≤" . "$\\\\le$")
|
|
("≥" . "$\\\\ge$")
|
|
("<" . "$<$")
|
|
("θ" . "$\\\\theta$")
|
|
("μ" . "$\\\\mu$")
|
|
("→" . "$\\\\rightarrow$")
|
|
("⇌" . "$\\\\leftrightharpoons$")
|
|
("×" . "$\\\\times$")
|
|
("°" . "$\\\\deg$")
|
|
("ş" . "{\\\\c{s}}")
|
|
("γ" . "$\\\\gamma$")
|
|
("ɣ" . "$\\\\gamma$")
|
|
("º" . "degC")
|
|
("η" . "$\\\\eta$")
|
|
("µ" . "$\\\\mu$")
|
|
("α" . "$\\\\alpha$")
|
|
("β" . "$\\\\beta$")
|
|
("ɛ" . "$\\\\epsilon$")
|
|
("Ⅵ" . "\\textrm{VI}")
|
|
("Ⅲ" . "\\textrm{III}")
|
|
("Ⅴ" . "\\textrm{V}")
|
|
("λ" . "$\\\\lambda$")
|
|
("π" . "$\\\\pi$")
|
|
("∞" . "$\\\\infty$")
|
|
("χ" . "$\\\\chi$")
|
|
("∼" . "\\\\textasciitilde{}")
|
|
("‑" . "\\\\textemdash{}")
|
|
(" " . " ")
|
|
("…" . "...")
|
|
("•" . "\\\\textbullet ")
|
|
;; I think these are non-ascii spaces. there seems to be more than one.
|
|
(" " . " ")
|
|
(" " . " ")
|
|
(" " . " ")
|
|
("–" . "-")
|
|
("−" . "-")
|
|
("–" . "-")
|
|
("—" . "-")
|
|
("‒" . "\\\\textemdash{}")
|
|
("‘" . "'")
|
|
("’" . "'")
|
|
("’" . "'")
|
|
("“" . "\"")
|
|
("’" . "'")
|
|
("”" . "\"")))
|
|
|
|
|
|
;;;###autoload
|
|
(defun org-ref-replace-nonascii ()
|
|
"Hook function to replace non-ascii characters in a bibtex entry."
|
|
(interactive)
|
|
(save-restriction
|
|
(bibtex-narrow-to-entry)
|
|
(goto-char (point-min))
|
|
(dolist (char (mapcar (lambda (x)
|
|
(car x))
|
|
org-ref-nonascii-latex-replacements))
|
|
(while (re-search-forward char nil t)
|
|
(replace-match (cdr (assoc char org-ref-nonascii-latex-replacements))))
|
|
(goto-char (point-min)))))
|
|
|
|
;;* Title case transformations
|
|
(defvar org-ref-lower-case-words
|
|
'("a" "an" "on" "and" "for"
|
|
"the" "of" "in")
|
|
"List of words to keep lowercase when changing case in a title.")
|
|
|
|
(defcustom org-ref-title-case-types '("article" "book")
|
|
"List of bibtex entry types in which the title will be converted to
|
|
title-case by org-ref-title-case."
|
|
:type '(repeat string)
|
|
:group 'org-ref-bibtex)
|
|
|
|
;;;###autoload
|
|
(defun org-ref-title-case (&optional key start end)
|
|
"Convert a bibtex entry title and booktitle to title-case.
|
|
Convert only if the entry type is a member of the list
|
|
`org-ref-title-case-types'. The arguments KEY, START and END are
|
|
optional, and are only there so you can use this function with
|
|
`bibtex-map-entries' to change all the title entries in articles and
|
|
books."
|
|
(interactive)
|
|
(dolist (field '("title" "booktitle"))
|
|
(save-restriction
|
|
(bibtex-narrow-to-entry)
|
|
(bibtex-beginning-of-entry)
|
|
;; Skip if field is not found in entry
|
|
(when (bibtex-search-forward-field field)
|
|
(let* ((title (bibtex-autokey-get-field field))
|
|
(words (split-string title))
|
|
(start 0))
|
|
(when
|
|
(member (downcase
|
|
(cdr (assoc "=type=" (bibtex-parse-entry))))
|
|
org-ref-title-case-types)
|
|
(setq words (mapcar
|
|
(lambda (word)
|
|
(cond
|
|
;; words containing more than one . are probably
|
|
;; abbreviations. We do not change those.
|
|
((with-temp-buffer
|
|
(insert word)
|
|
(goto-char (point-min))
|
|
(> (count-matches "\\.") 1))
|
|
word)
|
|
;; match words containing {} or \ which are probably
|
|
;; LaTeX or protected words, ignore
|
|
((string-match "\\$\\|{\\|}\\|(\\|)\\|\\\\" word)
|
|
word)
|
|
;; these words should not be capitalized, unless they
|
|
;; are the first word
|
|
((-contains? org-ref-lower-case-words
|
|
(s-downcase word))
|
|
(s-downcase word))
|
|
;; Words that are quoted
|
|
((s-starts-with? "\"" word)
|
|
(concat "\"" (s-capitalize (substring word 1))))
|
|
(t
|
|
(s-capitalize word))))
|
|
words))
|
|
|
|
;; Check if first word should be capitalized
|
|
(when (-contains? org-ref-lower-case-words (car words))
|
|
(setf (car words) (s-capitalize (car words))))
|
|
|
|
(setq title (mapconcat 'identity words " "))
|
|
|
|
;; Capitalize letters after a dash
|
|
(while
|
|
(string-match "[a-zA-Z]-\\([a-z]\\)" title start)
|
|
(let ((char (substring title (match-beginning 1) (match-end 1))))
|
|
(setf (substring title (match-beginning 1) (match-end 1))
|
|
(format "%s" (upcase char)))
|
|
(setq start (match-end 1))))
|
|
|
|
;; this is defined in doi-utils
|
|
(bibtex-set-field
|
|
field
|
|
title)
|
|
(bibtex-fill-entry)))))))
|
|
|
|
;;;###autoload
|
|
(defun org-ref-title-case-article (&optional key start end)
|
|
"Convert a bibtex entry article or book title to title-case.
|
|
The arguments KEY, START and END are optional, and are only there
|
|
so you can use this function with `bibtex-map-entries' to change
|
|
all the title entries in articles and books."
|
|
(interactive)
|
|
(let ((org-ref-title-case-types '("article")))
|
|
(org-ref-title-case)))
|
|
|
|
|
|
;;;###autoload
|
|
(defun org-ref-sentence-case-article (&optional key start end)
|
|
"Convert a bibtex entry article title to sentence-case.
|
|
The arguments KEY, START and END are optional, and are only there
|
|
so you can use this function with `bibtex-map-entries' to change
|
|
all the title entries in articles."
|
|
(interactive)
|
|
(bibtex-beginning-of-entry)
|
|
|
|
(let* ((title (bibtex-autokey-get-field "title"))
|
|
(words (split-string title))
|
|
(start 0))
|
|
(when
|
|
(string= "article"
|
|
(downcase
|
|
(cdr (assoc "=type="
|
|
(bibtex-parse-entry)))))
|
|
(setq words (mapcar
|
|
(lambda (word)
|
|
(if
|
|
;; match words containing {} or \ which are probably
|
|
;; LaTeX or protected words
|
|
(string-match "\\$\\|{\\|}\\|\\\\" word)
|
|
word
|
|
(s-downcase word)))
|
|
words))
|
|
|
|
;; capitalize first word
|
|
(setf (car words) (s-capitalize (car words)))
|
|
|
|
;; join the words
|
|
(setq title (mapconcat 'identity words " "))
|
|
|
|
;; capitalize a word after a :, eg. a subtitle, and protect it
|
|
(while
|
|
(string-match "[a-z]:\\s-+\\([A-Z]\\)" title start)
|
|
(let ((char (substring title (match-beginning 1) (match-end 1))))
|
|
(setf (substring title (match-beginning 1) (match-end 1))
|
|
(format "%s" (upcase char)))
|
|
(setq start (match-end 1))))
|
|
|
|
;; this is defined in doi-utils
|
|
(bibtex-set-field
|
|
"title" title)
|
|
|
|
;; clean and refill entry so it looks nice
|
|
(bibtex-clean-entry)
|
|
(bibtex-fill-entry))))
|
|
|
|
;;* Navigation in bibtex file
|
|
;;;###autoload
|
|
(defun org-ref-bibtex-next-entry (&optional n)
|
|
"Jump to the beginning of the next bibtex entry.
|
|
N is a prefix argument. If it is numeric, jump that many entries
|
|
forward. Negative numbers do nothing."
|
|
(interactive "P")
|
|
;; Note if we start at the beginning of an entry, nothing
|
|
;; happens. We need to move forward a char, and call again.
|
|
(when (= (point) (save-excursion
|
|
(bibtex-beginning-of-entry)))
|
|
(forward-char)
|
|
(org-ref-bibtex-next-entry))
|
|
|
|
;; search forward for an entry
|
|
(when
|
|
(re-search-forward bibtex-entry-head nil t (and (numberp n) n))
|
|
;; go to beginning of the entry
|
|
(bibtex-beginning-of-entry)))
|
|
|
|
|
|
;;;###autoload
|
|
(defun org-ref-bibtex-previous-entry (&optional n)
|
|
"Jump to beginning of the previous bibtex entry.
|
|
N is a prefix argument. If it is numeric, jump that many entries back."
|
|
(interactive "P")
|
|
(bibtex-beginning-of-entry)
|
|
(when
|
|
(re-search-backward bibtex-entry-head nil t (and (numberp n) n))
|
|
(bibtex-beginning-of-entry)))
|
|
|
|
|
|
(defun org-ref-bibtex-mode-keys ()
|
|
"Modify keymaps used by `bibtex-mode'."
|
|
(local-set-key (kbd "M-n") 'org-ref-bibtex-next-entry)
|
|
(local-set-key (kbd "M-p") 'org-ref-bibtex-previous-entry))
|
|
|
|
;; add to bibtex-mode-hook
|
|
(add-hook 'bibtex-mode-hook 'org-ref-bibtex-mode-keys)
|
|
|
|
;;* Functions to act on an entry with a doi
|
|
;;;###autoload
|
|
(defun org-ref-bibtex-entry-doi ()
|
|
"Get doi from entry at point."
|
|
(interactive)
|
|
(save-excursion
|
|
(bibtex-beginning-of-entry)
|
|
(when (not (looking-at bibtex-any-valid-entry-type))
|
|
(error "This entry does not appear to be a valid type."))
|
|
(let ((entry (bibtex-parse-entry t)))
|
|
(when (null entry)
|
|
(error "Unable to parse this bibtex entry."))
|
|
(reftex-get-bib-field "doi" entry))))
|
|
|
|
;; function that ensures that the url field of a bibtex entry is the
|
|
;; properly-formatted hyperlink of the DOI. See
|
|
;; http://blog.crossref.org/2016/09/new-crossref-doi-display-guidelines.html
|
|
;; for more information.
|
|
;;;###autoload
|
|
(defun org-ref-bibtex-format-url-if-doi ()
|
|
"Hook function to format url to follow the current DOI conventions."
|
|
(interactive)
|
|
(if (eq (org-ref-bibtex-entry-doi) "") nil
|
|
(let ((front-url "https://doi.org/")
|
|
(doi (org-ref-bibtex-entry-doi)))
|
|
(bibtex-set-field "url"
|
|
(concat front-url doi)))))
|
|
|
|
|
|
;;;###autoload
|
|
(defun org-ref-bibtex-wos ()
|
|
"Open bibtex entry in Web Of Science if there is a DOI."
|
|
(interactive)
|
|
(doi-utils-wos (org-ref-bibtex-entry-doi)))
|
|
|
|
|
|
;;;###autoload
|
|
(defun org-ref-bibtex-wos-citing ()
|
|
"Open citing articles for bibtex entry in Web Of Science if
|
|
there is a DOI."
|
|
(interactive)
|
|
(doi-utils-wos-citing (org-ref-bibtex-entry-doi)))
|
|
|
|
|
|
;;;###autoload
|
|
(defun org-ref-bibtex-wos-related ()
|
|
"Open related articles for bibtex entry in Web Of Science if
|
|
there is a DOI."
|
|
(interactive)
|
|
(doi-utils-wos-related (org-ref-bibtex-entry-doi)))
|
|
|
|
|
|
;;;###autoload
|
|
(defun org-ref-bibtex-crossref ()
|
|
"Open the bibtex entry in Crossref by its doi."
|
|
(interactive)
|
|
(doi-utils-crossref (org-ref-bibtex-entry-doi)))
|
|
|
|
|
|
;;;###autoload
|
|
(defun org-ref-bibtex-google-scholar ()
|
|
"Open the bibtex entry at point in google-scholar by its doi."
|
|
(interactive)
|
|
(let ((doi (org-ref-bibtex-entry-doi)))
|
|
(doi-utils-google-scholar
|
|
(if (string= "" doi)
|
|
(save-excursion
|
|
(bibtex-beginning-of-entry)
|
|
(reftex-get-bib-field "title" (bibtex-parse-entry t)))
|
|
doi))))
|
|
|
|
|
|
;;;###autoload
|
|
(defun org-ref-bibtex-pubmed ()
|
|
"Open the bibtex entry at point in Pubmed by its doi."
|
|
(interactive)
|
|
(doi-utils-pubmed (org-ref-bibtex-entry-doi)))
|
|
|
|
|
|
;;;###autoload
|
|
(defun org-ref-bibtex-pdf (&optional _)
|
|
"Open the pdf for the bibtex entry at point.
|
|
Thin wrapper to get `org-ref-bibtex' to open pdf, because it
|
|
calls functions with a DOI argument."
|
|
(interactive)
|
|
(org-ref-open-bibtex-pdf))
|
|
|
|
(defun org-ref-bibtex-get-file-move-func (prefix)
|
|
"Determine whether to use `rename-file' or `copy-file' for `org-ref-bibtex-assoc-pdf-with-entry'.
|
|
When called with a PREFIX argument,
|
|
`org-ref-bibtex-assoc-pdf-with-entry-move-function' switches to the
|
|
opposite function from that which is defined in
|
|
`org-ref-assoc-pdf-with-entry-move-function'."
|
|
(message (format "%s" prefix))
|
|
(if (eq prefix nil)
|
|
org-ref-bibtex-assoc-pdf-with-entry-move-function
|
|
(if (eq org-ref-bibtex-assoc-pdf-with-entry-move-function 'rename-file)
|
|
'copy-file
|
|
'rename-file)))
|
|
|
|
;;;###autoload
|
|
(defun org-ref-bibtex-assoc-pdf-with-entry (&optional prefix)
|
|
"Prompt for pdf associated with entry at point and rename it.
|
|
Check whether a pdf already exists in `org-ref-pdf-directory' with the
|
|
name '[bibtexkey].pdf'. If the file does not exist, rename it to
|
|
'[bibtexkey].pdf' using
|
|
`org-ref-bibtex-assoc-pdf-with-entry-move-function' and place it in
|
|
`org-ref-pdf-directory'. Optional PREFIX argument toggles between
|
|
`rename-file' and `copy-file'."
|
|
(interactive "P")
|
|
(save-excursion
|
|
(bibtex-beginning-of-entry)
|
|
(let* ((file (read-file-name "Select file associated with entry: "))
|
|
(bibtex-expand-strings t)
|
|
(entry (bibtex-parse-entry t))
|
|
(key (reftex-get-bib-field "=key=" entry))
|
|
(pdf (concat org-ref-pdf-directory (concat key ".pdf")))
|
|
(file-move-func (org-ref-bibtex-get-file-move-func prefix)))
|
|
(if (file-exists-p pdf)
|
|
(message (format "A file named %s already exists" pdf))
|
|
(progn
|
|
(funcall file-move-func file pdf)
|
|
(message (format "Created file %s" pdf)))))))
|
|
|
|
|
|
;;* Hydra menus
|
|
;;** Hydra menu for bibtex entries
|
|
;; hydra menu for actions on bibtex entries
|
|
(defhydra org-ref-bibtex-hydra (:color blue)
|
|
"
|
|
_p_: Open pdf _y_: Copy key _N_: New entry _w_: WOS
|
|
_b_: Open url _f_: Copy formatted entry _o_: Copy entry _c_: WOS citing
|
|
_r_: Refile entry _k_: Add keywords _d_: delete entry _a_: WOS related
|
|
_e_: Email entry _K_: Edit keywords _L_: clean entry _P_: Pubmed
|
|
_U_: Update entry _N_: New entry _R_: Crossref _g_: Google Scholar
|
|
_s_: Sort entry _a_: Remove nonascii _h_: helm-bibtex _q_: quit
|
|
_u_: Update field _F_: file funcs _A_: Assoc pdf with entry
|
|
_n_: Open notes _T_: Title case
|
|
_S_: Sentence case
|
|
"
|
|
("p" org-ref-open-bibtex-pdf)
|
|
("P" org-ref-bibtex-pubmed)
|
|
("w" org-ref-bibtex-wos)
|
|
("c" org-ref-bibtex-wos-citing)
|
|
("a" org-ref-bibtex-wos-related)
|
|
("R" org-ref-bibtex-crossref)
|
|
("g" org-ref-bibtex-google-scholar)
|
|
("N" org-ref-bibtex-new-entry/body)
|
|
("n" org-ref-open-bibtex-notes)
|
|
("o" (lambda ()
|
|
(interactive)
|
|
(bibtex-copy-entry-as-kill)
|
|
(message "Use %s to paste the entry"
|
|
(substitute-command-keys (format "\\[bibtex-yank]")))))
|
|
("d" bibtex-kill-entry)
|
|
("L" org-ref-clean-bibtex-entry)
|
|
("y" (save-excursion
|
|
(bibtex-beginning-of-entry)
|
|
(when (looking-at bibtex-entry-maybe-empty-head)
|
|
(kill-new (bibtex-key-in-head)))))
|
|
("f" (progn
|
|
(bibtex-beginning-of-entry)
|
|
(kill-new
|
|
(org-ref-format-entry
|
|
(cdr (assoc "=key=" (bibtex-parse-entry t)))))))
|
|
("k" helm-tag-bibtex-entry)
|
|
("K" (lambda ()
|
|
(interactive)
|
|
(org-ref-set-bibtex-keywords
|
|
(read-string "Keywords: "
|
|
(bibtex-autokey-get-field "keywords"))
|
|
t)))
|
|
("b" org-ref-open-in-browser)
|
|
("r" (lambda ()
|
|
(interactive)
|
|
(bibtex-beginning-of-entry)
|
|
(bibtex-kill-entry)
|
|
(find-file (completing-read
|
|
"Bibtex file: "
|
|
(f-entries "." (lambda (f) (f-ext? f "bib")))))
|
|
(goto-char (point-max))
|
|
(bibtex-yank)
|
|
(save-buffer)
|
|
(kill-buffer)))
|
|
("e" org-ref-email-bibtex-entry)
|
|
("U" (doi-utils-update-bibtex-entry-from-doi (org-ref-bibtex-entry-doi)))
|
|
("u" doi-utils-update-field)
|
|
("F" org-ref-bibtex-file/body)
|
|
("h" helm-bibtex)
|
|
("A" org-ref-bibtex-assoc-pdf-with-entry)
|
|
("a" org-ref-replace-nonascii)
|
|
("s" org-ref-sort-bibtex-entry)
|
|
("T" org-ref-title-case-article)
|
|
("S" org-ref-sentence-case-article)
|
|
("q" nil))
|
|
|
|
;; create key-chord and key binding for hydra
|
|
(when (and (featurep 'key-chord) org-ref-bibtex-hydra-key-chord)
|
|
(key-chord-define-global
|
|
org-ref-bibtex-hydra-key-chord
|
|
'org-ref-bibtex-hydra/body))
|
|
|
|
|
|
(when org-ref-bibtex-hydra-key-binding
|
|
(define-key bibtex-mode-map org-ref-bibtex-hydra-key-binding 'org-ref-bibtex-hydra/body))
|
|
|
|
;;** Hydra menu for new bibtex entries
|
|
;; A hydra for adding new bibtex entries.
|
|
(defhydra org-ref-bibtex-new-entry (:color blue)
|
|
"New Bibtex entry:"
|
|
("a" bibtex-Article "Article")
|
|
("b" bibtex-Book "Book")
|
|
("i" bibtex-InBook "In book")
|
|
("l" bibtex-Booklet "Booklet")
|
|
("P" bibtex-Proceedings "Proceedings")
|
|
("p" bibtex-InProceedings "In proceedings")
|
|
("m" bibtex-Misc "Misc.")
|
|
("M" bibtex-Manual "Manual")
|
|
("T" bibtex-PhdThesis "PhD Thesis")
|
|
("t" bibtex-MastersThesis "MS Thesis")
|
|
("R" bibtex-TechReport "Report")
|
|
("u" bibtex-Unpublished "unpublished")
|
|
("c" bibtex-InCollection "Article in collection")
|
|
("q" nil "quit"))
|
|
|
|
|
|
;;** Hydra menu of functions to act on a bibtex file.
|
|
(defhydra org-ref-bibtex-file (:color blue)
|
|
"Bibtex file functions: "
|
|
("v" bibtex-validate "Validate entries")
|
|
("s" bibtex-sort-buffer "Sort entries")
|
|
("r" bibtex-reformat "Reformat entries")
|
|
("c" bibtex-count-entries "Count entries")
|
|
("p" org-ref-build-full-bibliography "PDF bibliography"))
|
|
|
|
|
|
;;* DEPRECATED bibtex menu
|
|
(defvar org-ref-bibtex-menu-funcs '()
|
|
"Functions to run in doi menu.
|
|
Each entry is a list of (key menu-name function). The function
|
|
must take one argument, the doi. This is somewhat deprecated, as
|
|
I prefer the hydra interfaces above.")
|
|
|
|
(setq org-ref-bibtex-menu-funcs
|
|
'(("p" "df" org-ref-bibtex-pdf)
|
|
("C" "opy" (lambda (doi)
|
|
(kill-new (org-ref-bib-citation))
|
|
(bury-buffer)))
|
|
("w" "os" doi-utils-wos)
|
|
("c" "iting articles" doi-utils-wos-citing)
|
|
("r" "elated articles" doi-utils-wos-related)
|
|
("s" "Google Scholar" doi-utils-google-scholar)
|
|
("P" "Pubmed" doi-utils-pubmed)
|
|
("f" "CrossRef" doi-utils-crossref)))
|
|
|
|
;;;###autoload
|
|
(defun org-ref-bibtex ()
|
|
"Menu command to run in a bibtex entry.
|
|
Functions from `org-ref-bibtex-menu-funcs'. They all rely on the
|
|
entry having a doi."
|
|
(interactive)
|
|
;; construct menu string as a message
|
|
(message
|
|
(concat
|
|
(mapconcat
|
|
(lambda (tup)
|
|
(concat "[" (elt tup 0) "]"
|
|
(elt tup 1) " "))
|
|
org-ref-bibtex-menu-funcs "") ": "))
|
|
(let* ((input (read-char-exclusive))
|
|
(choice (assoc
|
|
(char-to-string input) org-ref-bibtex-menu-funcs)))
|
|
(when choice
|
|
(funcall
|
|
(elt
|
|
choice
|
|
2)
|
|
(org-ref-bibtex-entry-doi)))))
|
|
|
|
(defalias 'jb 'org-ref-bibtex)
|
|
|
|
|
|
;;;###autoload
|
|
(defun org-ref-email-bibtex-entry ()
|
|
"Email current bibtex entry at point and pdf if it exists."
|
|
(interactive)
|
|
|
|
(save-excursion
|
|
(bibtex-beginning-of-entry)
|
|
(let* ((key (reftex-get-bib-field "=key=" (bibtex-parse-entry t)))
|
|
pdf)
|
|
;; when we have org-ref defined we may have pdf to find.
|
|
(when (boundp 'org-ref-pdf-directory)
|
|
(setq pdf (expand-file-name
|
|
(concat key ".pdf")
|
|
org-ref-pdf-directory)))
|
|
(bibtex-copy-entry-as-kill)
|
|
(compose-mail)
|
|
(message-goto-body)
|
|
(insert (pop bibtex-entry-kill-ring))
|
|
(message-goto-subject)
|
|
(insert key)
|
|
(message "%s exists %s" pdf (file-exists-p pdf))
|
|
(when (file-exists-p pdf)
|
|
(mml-attach-file pdf))
|
|
(message-goto-to))))
|
|
|
|
;;* org-ref bibtex keywords
|
|
;; adapted from bibtex-utils.el
|
|
;; these are candidates for selecting keywords/tags
|
|
(defun org-ref-bibtex-keywords ()
|
|
"Get keywords defined in current bibtex file.
|
|
These are in the keywords field, and are comma or semicolon separated."
|
|
(save-excursion
|
|
(goto-char (point-min))
|
|
(let (keywords kstring)
|
|
(while (re-search-forward "^\\s-*keywords.*{\\([^}]+\\)}" nil t)
|
|
;; TWS - remove newlines/multiple spaces:
|
|
(setq kstring (replace-regexp-in-string
|
|
"[ \t\n]+" " "
|
|
(match-string 1)))
|
|
(mapc
|
|
(lambda (v)
|
|
(add-to-list 'keywords v t))
|
|
(split-string kstring "\\(,\\|;\\)[ \n]*\\|{\\|}" t)))
|
|
keywords)))
|
|
|
|
|
|
;;;###autoload
|
|
(defun org-ref-set-bibtex-keywords (keywords &optional arg)
|
|
"Add KEYWORDS to a bibtex entry.
|
|
If KEYWORDS is a list, it is converted to a comma-separated
|
|
string. The KEYWORDS are added to the beginning of the
|
|
field. Otherwise KEYWORDS should be a string of comma-separate
|
|
keywords. Optional argument ARG prefix arg to replace keywords."
|
|
(interactive
|
|
(list
|
|
(completing-read "Keyword: " (org-ref-bibtex-keywords))
|
|
current-prefix-arg))
|
|
(bibtex-set-field
|
|
"keywords"
|
|
(if arg
|
|
;; replace with arg
|
|
(if (listp keywords)
|
|
(mapconcat 'identity keywords ", ")
|
|
keywords)
|
|
;; else concatentate
|
|
(concat
|
|
(if (listp keywords)
|
|
(mapconcat 'identity keywords ", ")
|
|
keywords)
|
|
(when (not (string= "" (bibtex-autokey-get-field "keywords")))
|
|
(concat ", " (bibtex-autokey-get-field "keywords"))))))
|
|
(when (buffer-file-name)
|
|
(save-buffer)))
|
|
|
|
|
|
(defun org-ref-save-all-bibtex-buffers ()
|
|
"Save all bibtex-buffers."
|
|
(cl-loop for buffer in (buffer-list)
|
|
do
|
|
(with-current-buffer buffer
|
|
(when (and (buffer-file-name) (f-ext? (buffer-file-name) "bib"))
|
|
(save-buffer)))))
|
|
|
|
|
|
;;* org-ref bibtex cache
|
|
(defvar orhc-bibtex-cache-data
|
|
'((hashes . ())
|
|
(candidates . ()))
|
|
"Cache data as an alist.
|
|
'hashes is a list of cons cells (bibfile . hash)
|
|
'candidates is a list of cons cells (bibfile . candidates).
|
|
Stored persistently in `orhc-bibtex-cache-file'.")
|
|
|
|
|
|
(defvar orhc-bibtex-cache-file
|
|
"~/.orhc-bibtex-cache"
|
|
"File to store cached data in.")
|
|
|
|
|
|
(defvar org-ref-bibtex-files nil
|
|
"List of bibtex files to get entries from.
|
|
This is set internally.")
|
|
|
|
|
|
(defvar orhc-candidate-formats
|
|
'(("article" . "${pdf}${notes}|${=key=}| ${author}, ${title}, ${journal} (${year}). ${keywords}")
|
|
("book" . " |${=key=}| ${author}, ${title} (${year}) ${keywords}.")
|
|
("inbook" . " |${=key=}| ${author}, ${chapter} in ${title} (${year}) ${keywords}")
|
|
("techreport" . " |${=key=}| ${title}, ${institution} (${year}). ${keywords}")
|
|
("inproceedings" . " |${=key=}| ${author}, ${title} in ${booktitle} (${year}). ${keywords}")
|
|
("incollection" . " |${=key=}| ${author}, ${title} in ${booktitle} (${year}). ${keywords}")
|
|
("phdthesis" . " |${=key=}| ${author}, ${title}, ${school} (${year}). Phd thesis. ${keywords}")
|
|
("mastersthesis" . " |${=key=}| ${author}, ${title}, ${school} (${year}). MS thesis. ${keywords}")
|
|
("misc" . " |${=key=}| ${author}, ${title}")
|
|
("unpublished" . " |${=key=}| ${author}, ${title}"))
|
|
"Formats for candidates.
|
|
It is an alist of (=type= . s-format-string).")
|
|
|
|
|
|
;; when you load, we should check the hashes and files
|
|
(defun orhc-load-cache-file ()
|
|
"Load the cache file to set `orhc-bibtex-cache-data'."
|
|
(when (file-exists-p orhc-bibtex-cache-file)
|
|
(with-current-buffer (find-file-noselect orhc-bibtex-cache-file)
|
|
(goto-char (point-min))
|
|
(setq orhc-bibtex-cache-data (read (current-buffer))))
|
|
(when (find-buffer-visiting orhc-bibtex-cache-file)
|
|
(kill-buffer (find-buffer-visiting orhc-bibtex-cache-file)))))
|
|
|
|
|
|
(defun orhc-clear-cache ()
|
|
"Clear the cache and delete `orhc-bibtex-cache-file'."
|
|
(interactive)
|
|
(setq orhc-bibtex-cache-data '((hashes . nil)
|
|
(candidates . nil)))
|
|
(when (find-buffer-visiting orhc-bibtex-cache-file)
|
|
(kill-buffer (find-buffer-visiting orhc-bibtex-cache-file)))
|
|
(when (file-exists-p orhc-bibtex-cache-file)
|
|
(delete-file orhc-bibtex-cache-file))
|
|
(message "org-ref-helm-cite cache cleared."))
|
|
|
|
|
|
(defun orhc-bibtex-cache-up-to-date ()
|
|
"Return if bibtex caches are up to date.
|
|
This means the hash of each bibfile is equal to the one for it in
|
|
the cache."
|
|
(-all? 'identity
|
|
(cl-loop
|
|
for bibfile in org-ref-bibtex-files
|
|
collect
|
|
(string= (with-temp-buffer
|
|
(insert-file-contents bibfile)
|
|
(secure-hash 'sha256 (current-buffer)))
|
|
(or (cdr (assoc
|
|
bibfile
|
|
(cdr (assoc 'hashes orhc-bibtex-cache-data)))) "")))))
|
|
|
|
(defun orhc-bibtex-field-formatter (field entry)
|
|
"Format FIELD in a bibtex parsed ENTRY.
|
|
A few fields are treated specially, e.g. authors are replaced by
|
|
comma-separated list, and I put :: around keywords to make it
|
|
easier to search specifically for them."
|
|
(let ((s (replace-regexp-in-string
|
|
"^{\\|}$" ""
|
|
(replace-regexp-in-string
|
|
"[\n\t\s]+" " "
|
|
(or (cdr (assoc field entry))
|
|
(and (string= field "author")
|
|
(cdr (assoc "editor" entry)))
|
|
"")))))
|
|
(cond
|
|
((string= field "author")
|
|
(if org-ref-helm-cite-shorten-authors
|
|
;; copied from `helm-bibtex-shorten-authors'
|
|
(cl-loop for a in (s-split " and " s)
|
|
for p = (s-split "," a t)
|
|
for sep = "" then ", "
|
|
concat sep
|
|
if (eq 1 (length p))
|
|
concat (-last-item (s-split " +" (car p) t))
|
|
else
|
|
concat (car p))
|
|
(mapconcat 'identity (s-split " and " s) ", ")))
|
|
((string= field "keywords")
|
|
(if (> (length s) 0)
|
|
(mapconcat (lambda (keyword)
|
|
(concat ":" (s-trim keyword) ":"))
|
|
(s-split "," s)
|
|
" ")
|
|
""))
|
|
((string= field "pdf")
|
|
(if (file-exists-p (expand-file-name
|
|
(concat (cdr (assoc "=key=" entry)) ".pdf")
|
|
org-ref-pdf-directory))
|
|
"⌘"
|
|
" "))
|
|
((string= field "notes")
|
|
(if (file-exists-p (expand-file-name
|
|
(concat (cdr (assoc "=key=" entry)) ".org")
|
|
org-ref-notes-directory))
|
|
"✎"
|
|
" "))
|
|
;; catch all the other fields and just return them.
|
|
(t
|
|
s))))
|
|
|
|
(defun orhc-update-bibfile-cache (bibfile)
|
|
"Update cache for BIBFILE.
|
|
This generates the candidates for the file. Some of this code is
|
|
adapted from `helm-bibtex-parse-bibliography'. This function runs
|
|
when called, it resets the cache for the BIBFILE."
|
|
;; check if the bibfile is already open, and preserve this state. i.e. if it
|
|
;; is not open close it, and if it is leave it open.
|
|
(let ((bibfile-open (find-buffer-visiting bibfile)))
|
|
(with-current-buffer (find-file-noselect bibfile)
|
|
(bibtex-beginning-of-first-entry)
|
|
(message "Updating cache for %s" bibfile)
|
|
(let ((hash (secure-hash 'sha256 (current-buffer)))
|
|
(entries
|
|
(cl-loop
|
|
for entry-type = (parsebib-find-next-item)
|
|
while entry-type
|
|
unless (member-ignore-case entry-type
|
|
'("preamble" "string" "comment"))
|
|
collect
|
|
(let* ((entry (cl-loop for cons-cell in (parsebib-read-entry entry-type)
|
|
;; we remove all properties too. they
|
|
;; cause errors in reading/writing.
|
|
collect
|
|
(cons (substring-no-properties
|
|
(downcase (car cons-cell)))
|
|
(substring-no-properties
|
|
;; clumsy way to remove surrounding
|
|
;; brackets
|
|
(let ((s (cdr cons-cell)))
|
|
(if (or (and (s-starts-with? "{" s)
|
|
(s-ends-with? "}" s))
|
|
(and (s-starts-with? "\"" s)
|
|
(s-ends-with? "\"" s)))
|
|
(substring s 1 -1)
|
|
s))))))
|
|
;; (key (cdr (assoc "=key=" entry)))
|
|
)
|
|
(cons
|
|
;; this is the display string for helm. We try to use the formats
|
|
;; in `orhc-candidate-formats', but if there isn't one we just put
|
|
;; all the fields in.
|
|
(s-format
|
|
(or (cdr (assoc (downcase entry-type) orhc-candidate-formats))
|
|
(format "%s: %s" (cdr (assoc "=key=" entry)) entry))
|
|
'orhc-bibtex-field-formatter
|
|
entry)
|
|
;; this is the candidate that is returned, the entry a-list +
|
|
;; file and position.
|
|
(append entry (list (cons "bibfile" (buffer-file-name))
|
|
(cons "position" (point)))))))))
|
|
|
|
;; Now update the cache variables for hash and entries
|
|
(if (assoc bibfile (cdr (assoc 'candidates orhc-bibtex-cache-data)))
|
|
(setf (cdr (assoc bibfile
|
|
(cdr (assoc 'candidates orhc-bibtex-cache-data))))
|
|
entries)
|
|
(cl-pushnew (cons bibfile entries)
|
|
(cdr (assoc 'candidates orhc-bibtex-cache-data))))
|
|
(if (assoc bibfile (cdr (assoc 'hashes orhc-bibtex-cache-data)))
|
|
(setf (cdr (assoc
|
|
bibfile
|
|
(cdr (assoc 'hashes orhc-bibtex-cache-data))))
|
|
hash)
|
|
(cl-pushnew (cons bibfile hash)
|
|
(cdr (assoc 'hashes orhc-bibtex-cache-data))))
|
|
|
|
;; And save it to disk for persistent use
|
|
(with-temp-file orhc-bibtex-cache-file
|
|
(print orhc-bibtex-cache-data (current-buffer)))))
|
|
(unless bibfile-open (kill-buffer (find-buffer-visiting bibfile)))))
|
|
|
|
(defun orhc-update-bibtex-cache ()
|
|
"Conditionally update cache for all files in `org-ref-bibtex-files'.
|
|
Files that have the same hash as in the cache are not updated."
|
|
(cl-loop for bibfile in org-ref-bibtex-files
|
|
unless (string= (with-temp-buffer
|
|
(insert-file-contents bibfile)
|
|
(secure-hash 'sha256 (current-buffer)))
|
|
(or (cdr
|
|
(assoc bibfile
|
|
(cdr
|
|
(assoc 'hashes orhc-bibtex-cache-data))))
|
|
""))
|
|
do
|
|
(orhc-update-bibfile-cache bibfile)))
|
|
|
|
|
|
(defun orhc-helm-cite-describe-cache ()
|
|
"Show what is in the cache."
|
|
(interactive)
|
|
(let ((hash-cache (cdr (assoc 'hashes orhc-bibtex-cache-data)))
|
|
(candidates-cache (cdr (assoc 'candidates orhc-bibtex-cache-data))))
|
|
(message "%s\n\n%s"
|
|
(mapconcat (lambda (h)
|
|
(format "%s - %s" (car h) (cdr h)))
|
|
hash-cache "\n")
|
|
(mapconcat (lambda (c)
|
|
(format "%s - %s entries" (car c) (length (cdr c))))
|
|
candidates-cache "\n"))))
|
|
|
|
|
|
(defun orhc-bibtex-candidates ()
|
|
"Return the candidates from cache for files listed in `org-ref-bibtex-files'.
|
|
Update the cache if necessary."
|
|
;; this only does something when the cache is out of date
|
|
(org-ref-save-all-bibtex-buffers)
|
|
(orhc-update-bibtex-cache)
|
|
(let ((candidates (cdr (assoc 'candidates orhc-bibtex-cache-data))))
|
|
(apply 'append
|
|
(cl-loop for bibfile in org-ref-bibtex-files
|
|
collect (cdr (assoc bibfile candidates))))))
|
|
|
|
|
|
;; Now load files and update them if needed. We do this when you load the
|
|
;; library so they are available later.
|
|
(orhc-load-cache-file)
|
|
(orhc-update-bibtex-cache)
|
|
|
|
|
|
;;* org-ref bibtex formatted citation
|
|
|
|
(defun org-ref-format-bibtex-entry (entry)
|
|
"Return a formatted citation for the bibtex entry at point.
|
|
Formats are from `org-ref-formatted-citation-formats'. The
|
|
variable `org-ref-formatted-citation-backend' determines the set
|
|
of format strings used."
|
|
(save-excursion
|
|
(bibtex-beginning-of-entry)
|
|
(let* ((formats (cdr (assoc org-ref-formatted-citation-backend org-ref-formatted-citation-formats)))
|
|
(format-string)
|
|
(ref))
|
|
(if (null entry)
|
|
"!!! No entry found !!!"
|
|
(setq format-string (cdr (or (assoc (downcase (bibtex-completion-get-value "=type=" entry)) formats)
|
|
(assoc nil formats))))
|
|
(setq ref (s-format format-string 'bibtex-completion-apa-get-value entry))
|
|
(replace-regexp-in-string "\\([.?!]\\)\\." "\\1" ref)))))
|
|
|
|
|
|
(defun org-ref-format-entry (key)
|
|
"Returns a formatted bibtex entry for KEY."
|
|
(let* ((bibtex-completion-bibliography (org-ref-find-bibliography)))
|
|
(org-ref-format-bibtex-entry (ignore-errors (bibtex-completion-get-entry key)))))
|
|
|
|
|
|
(defun org-ref-format-bibtex-entry-at-point ()
|
|
"Return a formatted citation for the bibtex entry at point."
|
|
(save-excursion
|
|
(bibtex-beginning-of-entry)
|
|
(org-ref-format-bibtex-entry (bibtex-parse-entry t))))
|
|
|
|
|
|
;; ** using citeproc
|
|
(defun orhc-formatted-citation (entry)
|
|
"Get a formatted string for ENTRY."
|
|
(require 'unsrt)
|
|
(let* ((adaptive-fill-function '(lambda () " "))
|
|
(indent-tabs-mode nil)
|
|
(entry-type (downcase
|
|
(cdr (assoc "=type=" entry))))
|
|
(entry-styles (cdr (assoc 'entries bibliography-style)))
|
|
(entry-fields
|
|
(progn
|
|
(if (cdr (assoc (intern entry-type) entry-styles))
|
|
(cdr (assoc (intern entry-type) entry-styles))
|
|
(warn "%s not found. Using default." entry-type)
|
|
(cdr (assoc 't entry-styles)))))
|
|
(funcs (mapcar
|
|
(lambda (field)
|
|
(if (fboundp (intern
|
|
(format "orcp-%s" field)))
|
|
(intern
|
|
(format "orcp-%s" field))
|
|
;; No formatter found. just get the data
|
|
`(lambda (entry)
|
|
(orcp-get-entry-field
|
|
,(symbol-name field) entry))))
|
|
entry-fields)))
|
|
|
|
;; this is the entry. We do this in a buffer to make it
|
|
;; easy to indent, fill, etc...
|
|
(with-temp-buffer
|
|
(insert (mapconcat (lambda (field-func)
|
|
(funcall field-func entry))
|
|
funcs
|
|
""))
|
|
(buffer-string))))
|
|
|
|
;; * Extract bibtex blocks from an org-file
|
|
;;;###autoload
|
|
(defun org-ref-extract-bibtex-blocks (bibfile)
|
|
"Extract all bibtex blocks in buffer to BIBFILE.
|
|
If BIBFILE exists, append, unless you use a prefix arg (C-u), which
|
|
will clobber the file."
|
|
(interactive
|
|
(list (read-file-name "Bibfile: " nil nil nil
|
|
(file-name-nondirectory
|
|
(concat (file-name-sans-extension
|
|
(buffer-file-name))
|
|
".bib")))))
|
|
|
|
(let ((contents ""))
|
|
(when (and (file-exists-p bibfile)
|
|
(not current-prefix-arg))
|
|
(setq contents (with-temp-buffer
|
|
(insert-file-contents bibfile)
|
|
(buffer-string))))
|
|
|
|
(save-excursion
|
|
(goto-char (point-min))
|
|
(while (re-search-forward "#\\+BEGIN_SRC bibtex" nil t)
|
|
(setq contents
|
|
(concat
|
|
contents
|
|
(org-element-property :value (org-element-at-point))))))
|
|
|
|
(with-temp-file bibfile
|
|
(insert contents))))
|
|
|
|
(defun org-ref-bibtex-key-from-doi (doi &optional bib)
|
|
"Return a bibtex entry's key from a DOI.
|
|
BIB is an optional filename to get the entry from. Defaults to
|
|
the first entry of `org-ref-default-bibliography'."
|
|
(let ((bibfile (if bib bib (car org-ref-default-bibliography))))
|
|
(with-temp-buffer
|
|
(insert-file-contents (expand-file-name bibfile))
|
|
(search-forward doi)
|
|
(bibtex-beginning-of-entry)
|
|
(cdr (assoc "=key=" (bibtex-parse-entry))))))
|
|
|
|
;;* The end
|
|
(provide 'org-ref-bibtex)
|
|
|
|
;;; org-ref-bibtex.el ends here
|