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282 lines
9.5 KiB
282 lines
9.5 KiB
;;; org-ref-pdf.el --- Drag-n-drop PDF onto bibtex files -*- lexical-binding: t; -*-
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;; Copyright (C) 2015 John Kitchin
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;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
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;; Keywords:
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;; This program is free software; you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation, either version 3 of the License, or
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;; (at your option) any later version.
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;; This program is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU 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. If not, see <http://www.gnu.org/licenses/>.
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;;; Commentary:
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;; This library provides functions to enable drag-n-drop of pdfs onto a bibtex
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;; buffer to add bibtex entries to it.
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;; TODO: If no DOI is found, figure out a way to do a crossref/google query to
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;; get a doi. This needs a reliable title/citation.
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;;; Code:
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(require 'f)
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;; [2019-10-13 Sun] I am commenting this out for now. I added it for some
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;; reason, but I cannot figure out why. It is pretty slow to load, so since I
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;; don't know why it is here, I am commenting it out until it is obvious again.
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;; (require 'pdf-tools)
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(eval-when-compile
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(require 'cl-lib))
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(declare-function org-ref-bibtex-key-from-doi "org-ref-bibtex.el")
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(defgroup org-ref-pdf nil
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"Customization group for org-ref-pdf"
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:tag "Org Ref PDF"
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:group 'org-ref-pdf)
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(defcustom pdftotext-executable
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"pdftotext"
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"Executable for pdftotext. Set if the executable is not on your
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path, or you want to use another version."
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:type 'file
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:group 'org-ref-pdf)
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(defcustom org-ref-pdf-doi-regex
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"10\\.[0-9]\\{4,9\\}/[-+._;()/:A-Z0-9]+"
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"Regular expression to match DOIs in a pdf converted to text."
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:type 'regexp
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:group 'org-ref-pdf)
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(defcustom org-ref-pdf-to-bibtex-function
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'copy-file
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"Function for getting a pdf to the `org-ref-pdf-directory'.
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Defaults to `copy-file', but could also be `rename-file'."
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:type 'File :group 'org-ref-pdf)
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(defun org-ref-extract-doi-from-pdf (pdf)
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"Try to extract a doi from a PDF file.
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There may be more than one doi in the file. This function returns
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all the ones it finds based on two patterns: doi: up to a quote,
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bracket, space or end of line. dx.doi.org/up to a quote, bracket,
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space or end of line.
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If there is a trailing . we chomp it off. Returns a list of doi
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strings, or nil.
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"
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(with-temp-buffer
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(insert (shell-command-to-string (format "%s %s -"
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pdftotext-executable
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(shell-quote-argument (dnd-unescape-uri pdf)))))
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(goto-char (point-min))
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(let ((matches '()))
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(while (re-search-forward org-ref-pdf-doi-regex nil t)
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;; I don't know how to avoid a trailing . on some dois with the
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;; expression above, so if it is there, I chomp it off here.
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(let ((doi (match-string 0)))
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(when (s-ends-with? "." doi)
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(setq doi (substring doi 0 (- (length doi) 1))))
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(cl-pushnew doi matches :test #'equal)))
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matches)))
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(defun org-ref-pdf-doi-candidates (dois)
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"Generate candidate list for helm source.
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Used when multiple dois are found in a pdf file."
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(cl-loop for doi in dois
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collect
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(condition-case nil
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(cons
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(plist-get (doi-utils-get-json-metadata doi) :title)
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doi)
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(error (cons (format "%s read error" doi) doi)))))
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(defun org-ref-pdf-add-dois (_)
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"Add all entries for CANDIDATE in `helm-marked-candidates'."
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(cl-loop for doi in (helm-marked-candidates)
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do
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(doi-utils-add-bibtex-entry-from-doi
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doi
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(buffer-file-name))))
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;;;###autoload
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(defun org-ref-pdf-to-bibtex ()
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"Add pdf of current buffer to bib file and save pdf to
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`org-ref-default-bibliography'. The pdf should be open in Emacs
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using the `pdf-tools' package."
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(interactive)
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(when (not (f-ext? (downcase (buffer-file-name)) "pdf"))
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(error "Buffer is not a pdf file"))
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;; Get doi from pdf of current buffer
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(let* ((dois (org-ref-extract-doi-from-pdf (buffer-file-name)))
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(doi-utils-download-pdf nil)
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(doi (if (= 1 (length dois))
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(car dois)
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(completing-read "Select DOI: " dois))))
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;; Add bib entry from doi:
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(doi-utils-add-bibtex-entry-from-doi doi)
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;; Copy pdf to `org-ref-pdf-directory':
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(let ((key (org-ref-bibtex-key-from-doi doi)))
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(funcall org-ref-pdf-to-bibtex-function
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(buffer-file-name)
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(expand-file-name (format "%s.pdf" key)
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org-ref-pdf-directory)))))
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;;;###autoload
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;; (defun org-ref-pdf-dnd-func (event)
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;; "Drag-n-drop support to add a bibtex entry from a pdf file."
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;; (interactive "e")
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;; (goto-char (nth 1 (event-start event)))
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;; (x-focus-frame nil)
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;; (let* ((payload (car (last event)))
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;; (pdf (cadr payload))
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;; (dois (org-ref-extract-doi-from-pdf pdf)))
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;; (cond
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;; ((null dois)
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;; (message "No doi found in %s" pdf))
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;; ((= 1 (length dois))
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;; (doi-utils-add-bibtex-entry-from-doi
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;; (car dois)
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;; (buffer-file-name)))
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;; ;; Multiple DOIs found
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;; (t
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;; (helm :sources `((name . "Select a DOI")
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;; (candidates . ,(org-ref-pdf-doi-candidates dois))
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;; (action . org-ref-pdf-add-dois)))))))
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;; This isn't very flexible, as it hijacks all drag-n-drop events. I switched to
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;; using `dnd-protocol-alist'.
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;; (define-key bibtex-mode-map (kbd "<drag-n-drop>") 'org-ref-pdf-dnd-func)
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;; This is what the original dnd function was.
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;; (define-key bibtex-mode-map (kbd "<drag-n-drop>") 'ns-drag-n-drop)
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;; I replaced the functionality above with this new approach that leverages
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;; ns-drag-n-drop. An alternative approach would be to adapt the function above
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;; so that if the item dragged on wasn't a pdf, it would use another function.
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;; that is essentially what ns-drag-n-drop enables, multiple handlers for
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;; different uris that get dropped on the windwo.
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(defun org-ref-pdf-dnd-protocol (uri action)
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"Drag-n-drop protocol.
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PDF will be a string like file:path.
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ACTION is what to do. It is required for `dnd-protocol-alist'.
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This function should only apply when in a bibtex file."
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(if (and (buffer-file-name)
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(f-ext? (buffer-file-name) "bib"))
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(let* ((path (substring uri 5))
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dois)
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(cond
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((f-ext? path "pdf")
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(setq dois (org-ref-extract-doi-from-pdf
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path))
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(cond
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((null dois)
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(message "No doi found in %s" path)
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nil)
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((= 1 (length dois))
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;; we do not need to get the pdf, since we have one.
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(let ((doi-utils-download-pdf nil))
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(doi-utils-add-bibtex-entry-from-doi
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(car dois)
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(buffer-file-name))
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;; we should copy the pdf to the pdf directory though
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(let ((key (cdr (assoc "=key=" (bibtex-parse-entry)))))
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(copy-file (dnd-unescape-uri path) (expand-file-name (format "%s.pdf" key) org-ref-pdf-directory))))
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action)
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;; Multiple DOIs found
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(t
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(helm :sources `((name . "Select a DOI")
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(candidates . ,(org-ref-pdf-doi-candidates dois))
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(action . org-ref-pdf-add-dois)))
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action)))
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;; drag a bib file on and add contents to the end of the file.
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((f-ext? path "bib")
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(goto-char (point-max))
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(insert "\n")
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(insert-file-contents path))))
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;; ignoring. pass back to dnd. Copied from `org-download-dnd'. Apparently
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;; returning nil does not do this.
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(let ((dnd-protocol-alist
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(rassq-delete-all
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'org-ref-pdf-dnd-protocol
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(copy-alist dnd-protocol-alist))))
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(dnd-handle-one-url nil action uri))))
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(add-to-list 'dnd-protocol-alist '("^file:" . org-ref-pdf-dnd-protocol))
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;;;###autoload
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(defun org-ref-pdf-dir-to-bibtex (bibfile directory)
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"Create BIBFILE from pdf files in DIRECTORY."
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(interactive (list
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(read-file-name "Bibtex file: ")
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(read-directory-name "Directory: ")))
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(find-file bibfile)
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(goto-char (point-max))
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(cl-loop for pdf in (f-entries directory (lambda (f) (f-ext? f "pdf")))
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do
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(goto-char (point-max))
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(let ((dois (org-ref-extract-doi-from-pdf pdf)))
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(cond
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((null dois)
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(insert (format "%% No doi found to create entry in %s.\n" pdf)))
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((= 1 (length dois))
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(doi-utils-add-bibtex-entry-from-doi
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(car dois)
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(buffer-file-name))
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(bibtex-beginning-of-entry)
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(insert (format "%% [[file:%s]]\n" pdf)))
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;; Multiple DOIs found
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(t
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(insert (format "%% Multiple dois found in %s\n" pdf))
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(helm :sources `((name . "Select a DOI")
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(candidates . ,(org-ref-pdf-doi-candidates dois))
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(action . org-ref-pdf-add-dois))))))))
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;;;###autoload
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(defun org-ref-pdf-debug-pdf (pdf-file)
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"Try to debug getting a doi from a pdf.
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Opens a buffer with the pdf converted to text, and `occur' on the
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variable `org-ref-pdf-doi-regex'."
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(interactive "fPDF: ")
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(switch-to-buffer (get-buffer-create "*org-ref-pdf debug*"))
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(erase-buffer)
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(insert (shell-command-to-string (format "%s %s -"
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pdftotext-executable
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(shell-quote-argument pdf-file))))
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(goto-char (point-min))
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(highlight-regexp org-ref-pdf-doi-regex)
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(occur org-ref-pdf-doi-regex)
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(switch-to-buffer-other-window "*Occur*"))
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;;;###autoload
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(defun org-ref-pdf-crossref-lookup ()
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"Lookup highlighted text in PDFView in CrossRef."
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(interactive)
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(require 'pdf-view)
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(pdf-view-assert-active-region)
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(let* ((txt (pdf-view-active-region-text)))
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(pdf-view-deactivate-region)
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(crossref-lookup (mapconcat 'identity txt " \n"))))
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(provide 'org-ref-pdf)
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;;; org-ref-pdf.el ends here
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