eBib-Biblio interface, aka. Mendeley for Emacs

REGEDIT4

[HKEY_CLASSES_ROOT\org-protocol]
@="URL:Org Protocol"
"URL Protocol"=""
[HKEY_CLASSES_ROOT\org-protocol\shell]
[HKEY_CLASSES_ROOT\org-protocol\shell\open]
[HKEY_CLASSES_ROOT\org-protocol\shell\open\command]
@="emacsclientw.exe \"%1\""

(use-package ebib-biblio-interface
  :after (ebib biblio org-protocol)
  :load-path "location/of/the/library/")

javascript:location.href='org-protocol://ebib-biblio-interface?url='+encodeURIComponent(location.href)

;;; -*- lexical-binding: t -*-
;;;
;;; ebib-biblio-interface.el --- downloading bibtex files from webpages
;;;
;;; Copyright (C) 2020 Juan Jose Garcia-Ripoll
;;
;; All rights reserved.

;; Redistribution and use in source and binary forms, with or without
;; modification, are permitted provided that the following conditions are met:
;; 1. Redistributions of source code must retain the above copyright
;;    notice, this list of conditions and the following disclaimer.
;; 2. Redistributions in binary form must reproduce the above copyright
;;    notice, this list of conditions and the following disclaimer in the
;;    documentation  and/or other materials provided with the distribution.
;; 3. Neither the names of the copyright holders nor the names of any
;;    contributors may be used to endorse or promote products derived from
;;    this software without specific prior written permission.
;;
;; THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
;; AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
;; IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
;; ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
;; LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
;; CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
;; SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
;; INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
;; CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
;; ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
;; POSSIBILITY OF SUCH DAMAGE.
;;
;;; Version: 0.1
;;; Author: Juan Jose Garcia-Ripoll <[email protected]>
;;; Keywords: org mode, plain text, notes, Deft, Simplenote, Notational Velocity

;; This file is not part of GNU Emacs.

(require 'org-protocol)
(require 'biblio)

;;
;; org-protocol://ebib-biblio-interface?url=encoded-url-text
;; Register Firefox bookmark with the format
;; javascript:location.href='org-protocol://ebib-biblio-interface?url='+encodeURIComponent(location.href)
;;
(defun ebib-biblio-interface-handler (fname)
  (message "Received fname %S" fname)
  (let* ((splitparts (org-protocol-parse-parameters fname nil '(:url)))
         (uri (org-protocol-sanitize-uri (plist-get splitparts :url)))
         dois)
    (raise-frame)
    (ebib-biblio-interface-handler--inner uri)))

(defun ebib-biblio-interface-handler--inner (uri)
  "Given the URI of a manuscript, guess its DOI or find it out in the webpage
content, and query CrossRef for that manuscript, offering the user the
possibility to save that record.

Example of use:

(ebib-biblio-interface-handler--inner \"https://www.nature.com/articles/s41598-020-63093-6\")
"
  (message "Registering bibliography item with url %s" uri)
  (let ((biblio-synchronous t))
    (cond ((string-match "http[s]*://arxiv.org/abs" uri)
           (message "Found arXiv reference %s" uri)
           (biblio-arxiv-lookup
            (replace-regexp-in-string "http[s]*://arxiv.org/\\(abs\\|pdf\\)/" "" uri)))
          ((setq dois (ebib-biblio-interface-guess-doi uri))
           (message "Found DOI %s" dois)
           ;; When there is a single DOI, we can directly try to download
           ;; the Bibtex record
           (biblio-doi-forward-bibtex (biblio-cleanup-doi dois)
                                      'ebib-capture-raw-bibtex))
          ((setq dois (ebib-biblio-interface-search-dois-in-url uri))
           (message "Found DOI's %s" dois)
           (if (cdr dois)
               ;; Only use CrossRef when we really have more than one DOI
               ;; to choose from.
               (biblio-multiple-doi-lookup dois)
             (biblio-doi-forward-bibtex (biblio-cleanup-doi (car dois))
                                        'ebib-capture-raw-bibtex)))
          (t
           (message "No DOI's found in %s" uri))))
  ;; Return NIL to prevent any buffer from being opened
  nil)

(unless (assoc "ebib-biblio-interface" org-protocol-protocol-alist)
  (add-to-list 'org-protocol-protocol-alist
               '("ebib-biblio-interface"
                 :protocol "ebib-biblio-interface"
                 :function ebib-biblio-interface-handler)))

;; We bind globally the key C-i to the function that saves biblio
;; records to ebib.
(define-key biblio-selection-mode-map [?\C-i] 'ebib-biblio-interface-export-record-and-quit)

(defun ebib-biblio-interface-export-record-and-quit ()
  (interactive)
  (biblio--selection-forward-bibtex
   (lambda (entry metadata)
     (quit-window)
     (ebib-capture-raw-bibtex entry))))

(defun biblio-crossref-doi--url (query)
  "Create a CrossRef url to look up DOI."
  (format "http://api.crossref.org/works?filter=doi:%s%s"
          (biblio-cleanup-doi query)
          (if biblio-crossref-user-email-address
              (format "&mailto=%s" (url-encode-url biblio-crossref-user-email-address)) "")))

(defun biblio-crossref-doi-backend (command &optional arg &rest more)
  "A CrossRef backend querying multiple DOI's.
COMMAND, ARG, MORE: See `biblio-backends'."
  (pcase command
    (`name "CrossRef DOI's")
    (`prompt "CrossRef DOI's: ")
    (`url (biblio-crossref-doi--url arg))
    (`parse-buffer (biblio-crossref--parse-search-results))
    (`forward-bibtex (biblio-crossref--forward-bibtex arg (car more)))
    (`register (add-to-list 'biblio-backends #'biblio-crossref-backend))))

(defun biblio-crossref-doi-lookup (&optional query)
  "Start a CrossRef search for DOI, prompting if needed."
  (interactive "MDOI: ")
  (biblio-lookup #'biblio-crossref-doi-backend query))

(defun biblio-combined-backend (command &optional arg &rest more)
  "A CrossRef backend querying multiple DOI's.
COMMAND, ARG, MORE: See `biblio-backends'."
  (pcase command
    (`name "Combined backend")
    (`prompt "Combined backend query: ")
    (`url "")
    (`parse-buffer nil)
    (`forward-bibtex nil)
    (`register nil)))

(defun biblio--lookup-n (backend-query-pairs &optional results-buffer results)
  (unless results-buffer
    (setq results-buffer
          (biblio--make-results-buffer (current-buffer) "multiple query" 'biblio-combined-backend)))
  (if backend-query-pairs
      (let ((backend (caar backend-query-pairs))
            (query (cdar backend-query-pairs)))
        (biblio-url-retrieve
         (funcall backend 'url query)
         (biblio-generic-url-callback
          (lambda ()
            (biblio--lookup-n (rest backend-query-pairs) results-buffer
                              (append results (biblio--tag-backend backend (funcall backend 'parse-buffer))))))))
    (message "Tip: learn to browse results with `h'")
    (with-current-buffer results-buffer
      (biblio-insert-results results "Combined results"))))

(defun biblio-multiple-doi-lookup (doi-list)
  (biblio--lookup-n (mapcar #'(lambda (x) (cons 'biblio-crossref-doi-backend x))
                            doi-list)))

(defun ebib-biblio-interface-delete-duplicates (list)
  (let ((output nil))
    (dolist (elt list output)
  (unless (member elt output)
    (push elt output)))))

(defun ebib-biblio-interface-search-dois-in-url (url)
  "Search all DOI urls or codes in a web page, using formats that
are know from journals.

Example:
(ebib-biblio-interface-search-dois-in-url \"https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.85.82\")
=> '(\"10.1103/PhysRevLett.85.82\")
"
  (with-current-buffer (url-retrieve-synchronously url)
    (message "%S" (point-min) (point-max))
    (prog1 (ebib-biblio-interface-delete-duplicates
        (or
         ;; APS
         (ebib-biblio-interface-collect-regexps
          "<meta[ ]*content=\"doi:\\([^\"]+\\)\"" 1)
         ;; SIAM
         (ebib-biblio-interface-collect-regexps
          "<meta[ ]*name=\"dc.Identifier\"[ ]*scheme=\"doi\"[ ]*content=\"\\([^\"]+\\)" 1)
         ;; Quantum Journal
         (ebib-biblio-interface-collect-regexps
          "<meta[ ]*name=\"\\(citation_doi\\|doi\\)\"[ ]*content=\"\\([^\"]+\\)\"" 2)
         ;; IEEE
         (ebib-biblio-interface-collect-regexps
          ",\"doi\":\"\\([^\"]+\\)\"" 1)
         ;; Look for all DOI's
         (ebib-biblio-interface-collect-regexps
          "[\"']https?://\\(dx.\\)?doi.org/\\(?1:[^\"'& ]+\\)[\"']" 1)))
  (kill-buffer))))

(defvar ebib-biblio-interface-url-patterns
  '(;; IOP
    ("iopscience.iop.org/article/\\(?1:[0-9]+\\.[0-9]+\\(/[a-zA-Z0-9-]+\\)+\\)\\(/meta\\|/full\|pdf\\)")
    ("iopscience.iop.org/article/\\(?1:[0-9]+\\.[0-9]+\\(/[a-zA-Z0-9-]+\\)+\\)")
    ;; Springer
    ("link.springer.com/article/\\([0-9]+\\.[0-9]+/[^/]+\\)")
    ;; American Physical Society
    ("journals.aps.org/\\(pr[abcdex]\\|prappl\\|prx\\|prxquantum\\|rmp\\)/abstract/\\(?1:[^/]+/[^/]+\\)")
    ;; Wiley Online Library
    ("onlinelibrary.wiley.com/doi/full/\\(?1:[0-9]+\\.[0-9]+\\/[^/]+\\)")
    ;; Frontiers
    ("www.frontiersin.org/articles/\\(?1:[0-9]+\\.[0-9]+/[^/]+\\)/")
    ;; Nature, Scientific Reports, and others
    ("www.nature.com/articles/\\(?1:[0-9a-z-]+\\)" "10.1038/"))
  "Patterns to recognize DOI's from the URL's of scientific journals.")

(defun ebib-biblio-interface-guess-doi (url)
  "Guess the DOI directly from the URL, saving us some time.

Examples:

(ebib-biblio-interface-guess-doi
  \"https://iopscience.iop.org/article/10.1209/0295-5075/125/30004/meta\")
  => \"https://dx.doi.org/10.1209/0295-5075/125/30004\"
(ebib-biblio-interface-guess-doi
  \"https://journals.aps.org/rmp/abstract/10.1103/RevModPhys.92.011003\")
  => \"https://dx.doi.org/10.1103/RevModPhys.92.011003\"
(ebib-biblio-interface-guess-doi
  \"https://www.nature.com/articles/d41586-020-00926-4\")
  => \"https://dx.doi.org/10.1038/d41586-020-00926-4\"
"
  (with-temp-buffer
    ;; Sometimes, %2F appear in links instead of /, specially in
    ;; Springer
    (insert (url-unhex-string url))
    (catch 'found
      (dolist (record ebib-biblio-interface-url-patterns)
        (let ((pattern (concat "^https?://" (car record)))
              (prefix (or (cadr record) "")))
          (goto-char (point-min))
          (if (re-search-forward pattern nil t)
              (let ((doi (match-string-no-properties 1)))
                (when doi
                  (throw 'found (concat "https://dx.doi.org/" prefix doi))))))
      nil))))

(defun ebib-biblio-interface-collect-regexps (regexp &optional count from-point)
  "Return a list with all matches of 'regexp', either from the
beginning or from the current position in the buffer. By default
it returns the whole match, but 'count' may be a number denoting
a parenthetical expression."
  (let ((output '())
        (position (point)))
    (unless from-point
      (goto-char 0))
    (while (re-search-forward regexp nil t)
      (push (match-string-no-properties (or count 1)) output))
    (goto-char position)
    output))

(defvar ebib-capture-mode-map
  (let ((map (make-sparse-keymap)))
    (define-key map "\C-c\C-c" #'ebib-capture-finalize)
    (define-key map "\C-c\C-k" #'ebib-capture-kill)
    map)
  "Keymap for `ebib-capture-mode', a minor mode.
  Use this map to set additional keybindings for when Org mode is used
  for a capture buffer.")

(defvar ebib-capture-mode-hook nil
  "Hook for the `ebib-capture-mode' minor mode.")

(define-minor-mode ebib-capture-mode
  "Minor mode for special key bindings in a capture buffer.

  Turning on this mode runs the normal hook `ebib-capture-mode-hook'."
  nil " Cap" ebib-capture-mode-map
  (setq-local
   header-line-format
   (substitute-command-keys
    "\\<ebib-capture-mode-map>Capture buffer.  Finish \
  `\\[ebib-capture-finalize]', abort `\\[ebib-capture-kill]'.")))

(defun ebib-capture-kill ()
  "Abort the current capture process."
  (interactive)
  ;; FIXME: This does not do the right thing, we need to remove the
  ;; new stuff by hand it is easy: undo, then kill the buffer
  (quit-window t))

(defun ebib-capture-finalize (&optional prefix)
  "Save entries and finalize. Use C-u as prefix to also switch to ebib."
  (interactive "P")
  (ebib--execute-when
    ((or slave-db filtered-db)
     (error "[Ebib] Cannot merge into a filtered or a slave database"))
    (real-db
     (let* ((ebib--cur-db (ebib-select-database))
            (keys (ebib-capture-consistent-buffer)))
       (when keys
         (let ((result (ebib--bib-find-bibtex-entries ebib--cur-db nil)))
           (ebib--log 'message "%d entries, %d @Strings and %s @Preamble found in file."
                      (car result)
                      (cadr result)
                      (if (nth 2 result) "a" "no")))
         (ebib--set-modified t ebib--cur-db)
         (ebib-capture-kill)
         (ebib--update-buffers)
         (when prefix
           (ebib)
           (ebib--goto-entry-in-index (car keys))
           (ebib--update-buffers)))))
    (default (beep))))

(defun ebib-select-database ()
  (let ((l (length ebib--databases)))
    (if (<= l 1)
        ebib--cur-db
      (let* ((pairs (mapcar (lambda (db) (cons (file-name-base (cdr (assq 'filename db))) db))
                            ebib--databases))
             (cur-db-name (file-name-base (cdr (assq 'filename ebib--cur-db))))
             (names (mapcar 'car pairs))
             (choice (completing-read "Ebib database: " names nil t cur-db-name
                                      nil cur-db-name)))
        (cdr (assoc choice pairs))))))

(defun ebib-capture-consistent-buffer ()
  (let ((db (ebib-db-new-database))
        (duplicates '())
        (originals '()))
    (let ((result (ebib--bib-find-bibtex-entries db nil)))
      (if (zerop (car result))
          (message "No entries found")
        (maphash
         (lambda (key value)
           (if (ebib-db-get-entry key ebib--cur-db t)
               (push key duplicates)
             (push key originals)))
         (ebib-db-val 'entries db))
        (when duplicates
          (message "Found duplicate keys: %S" duplicates)
          (goto-char 0)
          (search-forward (car duplicates))
          (setq originals nil))
        originals))))

(defun ebib-capture-raw-bibtex (entry)
  (require 'ebib)
  (unless ebib--cur-db
    (ebib))
  (with-current-buffer (get-buffer-create "*Biblio entry*")
    (erase-buffer)
    (insert entry)
    (bibtex-mode)
    (bibtex-set-dialect "BibTeX")
    (ebib-capture-mode)
    (goto-char 0)
    (search-forward "{" nil t)
    (pop-to-buffer (current-buffer))
    (current-buffer)))

(defun ebib-capture-selection-entry (start end)
  (interactive "r")
  (ebib-capture-raw-bibtex (buffer-substring start end)))

(when nil
(ebib-capture-raw-bibtex "@Article{Garc_a_Ripoll_1999,
  author       = {García-Ripoll, Juan J. and Pérez-García, Víctor
                  M. and Torres, Pedro},
  title        = {Extended Parametric Resonances in Nonlinear
                  Schrödinger Systems},
  year         = 1999,
  volume       = 83,
  number       = 9,
  month        = {Aug},
  pages        = {1715–1718},
  issn         = {1079-7114},
  doi          = {10.1103/physrevlett.83.1715},
  url          = {http://dx.doi.org/10.1103/physrevlett.83.1715},
  journal      = {Physical Review Letters},
  publisher    = {American Physical Society (APS)}
}"))

(define-key ebib-index-mode-map (kbd "C-x g") 'ebib-browse-google-scholar)

(defun ebib-browse-google-scholar ()
  "Search this entry in Google Scholar. If the DOI is known,
use it as match. Otherwise try the title."
  (interactive)
  (ebib--execute-when
    (entries
     (let ((key (ebib--get-key-at-point))
           (value nil))
       (if (setq value (ebib-get-field-value ebib-doi-field key ebib--cur-db 'noerror 'unbraced 'xref))
           (with-temp-buffer
             (insert value)
             (goto-char (point-min))
             (while (re-search-forward "\\([ \n\t]+\\|https?://\\(dx.\\)doi.org/\\)" nil t)
               (replace-match ""))
             (setq value (concat "doi:" (buffer-substring-no-properties (point-min) (point-max)))))
         (setq value (concat "title:\"" (ebib-get-field-value "title" key ebib--cur-db 'noerror 'ubraced 'xref) "\"")))
       (ebib--call-browser (concat "https://scholar.google.com/scholar?q="
                                   (url-hexify-string value)))))
    (default
      (beep))))

(provide 'ebib-biblio-interface)