daniel/emacs
1
2
Fork 0
Code Issues 7 Pull Requests Projects Releases Wiki Activity
Files
059fa065720d0a618e0e007c7a7dccbfbb5d2f91
emacs/lisp/org-ref/doi-utils.el
Daniel Weschke dbbae92267 update packages
2025-11-25 19:52:03 +01:00

1738 lines
68 KiB
EmacsLisp
Raw Blame History

This file contains ambiguous Unicode characters
This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.
;;; doi-utils.el --- DOI utilities for making bibtex entries -*- lexical-binding: t; -*-
;; Copyright (C) 2015-2021 John Kitchin
;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
;; Keywords: convenience
;; Package-Requires: ((org-ref))
;; This program is free software; you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation, either version 3 of the License, or
;; (at your option) any later version.
;; This program is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;; GNU General Public License for more details.
;; You should have received a copy of the GNU General Public License
;; along with this program. If not, see <http://www.gnu.org/licenses/>.
;;; Commentary:
;; This package provides functionality to download PDFs and bibtex entries from
;; a DOI, as well as to update a bibtex entry from a DOI. It depends slightly
;; on org-ref, to determine where to save pdf files too, and where to insert
;; bibtex entries in the default bibliography.
;; The principle commands you will use from here are:
;; - doi-utils-get-bibtex-entry-pdf with the cursor in a bibtex entry.
;; - doi-utils-insert-bibtex-entry-from-doi to insert a bibtex entry at your cursor, clean it and try to get a pdf.
;; - doi-utils-add-bibtex-entry-from-doi to add an entry to your default bibliography (cleaned with pdf if possible).
;; - doi-utils-update-bibtex-entry-from-doi with cursor in an entry to update its fields.
;;; Code:
(defvar url-http-end-of-headers)
(declare-function org-ref-find-bibliography "org-ref-core")
(declare-function org-ref-clean-bibtex-entry "org-ref-core")
(declare-function bibtex-completion-edit-notes "bibtex-completion")
(declare-function org-bibtex-yank "org-bibtex")
(declare-function org-ref-possible-bibfiles "org-ref-core")
(declare-function org-ref-normalize-bibtex-completion-bibliography "org-ref-utils")
(declare-function org-ref--file-ext-p "org-ref-utils")
(declare-function org-ref--directory-files "org-ref-utils")
(eval-when-compile
(require 'cl-lib))
(require 'bibtex)
(require 'json)
(require 'org) ; org-add-link-type
(or (require 'ol-bibtex nil t)
(require 'org-bibtex)) ; org-bibtex-yank
(require 'url-http)
(require 'url-handlers)
(require 'org-ref-utils)
(require 'transient)
;;* Customization
(defgroup doi-utils nil
"Customization group for doi-utils."
:tag "DOI utils"
:group 'doi-utils)
(defcustom doi-utils-download-pdf
t
"Try to download PDFs when adding bibtex entries when non-nil."
:type 'boolean
:group 'doi-utils)
(defcustom doi-utils-open-pdf-after-download
nil
"Open PDF after adding bibtex entries."
:type 'boolean
:group 'doi-utils)
(defcustom doi-utils-timestamp-field
"DATE_ADDED"
"The bibtex field to store the date when an entry has been added."
:type 'string
:group 'doi-utils)
(defcustom doi-utils-timestamp-format-function
'current-time-string
"The function to format the timestamp for a bibtex entry.
Set to a function that returns nil to avoid setting timestamps in the entries.
e.g. (lambda () nil)"
:type 'function
:group 'doi-utils)
(defcustom doi-utils-dx-doi-org-url
"https://doi.org/"
"Base url to retrieve doi metadata from. A trailing / is required."
:type 'string
:group 'doi-utils)
(defcustom doi-utils-metadata-function 'doi-utils-get-json-metadata
"Function for retrieving json metadata from `doi-utils-dx-doi-org-url'.
The default is `doi-utils-get-json-metadata', but it sometimes
fails with a proxy. An alternative is
`doi-utils-get-json-metadata-curl' which requires an external
program to use curl."
:type 'function
:group 'doi-utils)
(defcustom doi-utils-async-download t
"Use `doi-utils-async-download-pdf' to get pdfs asynchrounously.
If nil use `doi-utils-get-bibtex-entry-pdf' synchronously."
:type 'boolean
:group 'doi-utils)
(defun doi-utils-pdf-filename-from-key ()
"Generate PDF filename from bibtex entry key.
This is the default function for `doi-utils-pdf-filename-function'.
Returns the bibtex entry key as the filename (without extension or path)."
(cdr (assoc "=key=" (bibtex-parse-entry))))
(defcustom doi-utils-pdf-filename-function
'doi-utils-pdf-filename-from-key
"Function to generate PDF filename from bibtex entry.
The function is called with no arguments while point is in the bibtex
entry, and should return a string to use as the PDF filename (without
the .pdf extension or directory path).
The directory path is determined separately by `bibtex-completion-library-path'.
The default function uses the bibtex entry key as the filename.
Example: To use the title field as the filename:
(setq doi-utils-pdf-filename-function
(lambda () (bibtex-autokey-get-field \"title\")))
Note: The function is responsible for ensuring the returned filename
is valid for the filesystem. Special characters in fields like title
may cause issues on some systems."
:type 'function
:group 'doi-utils)
;;* Getting pdf files from a DOI
;; The idea here is simple. When you visit http://dx.doi.org/doi or
;; https://doi.org/doi, you get redirected to the journal site. Once you have
;; the url for the article, you can usually compute the url to the pdf, or find
;; it in the page. Then you simply download it.
;; There are some subtleties in doing this that are described here. To get the
;; redirect, we have to use url-retrieve, and a callback function. The callback
;; does not return anything, so we communicate through global variables.
;; url-retrieve is asynchronous, so we have to make sure to wait for it to
;; finish.
(defvar *doi-utils-waiting* t
"Stores waiting state for url retrieval.")
(defvar *doi-utils-redirect* nil
"Stores redirect url from a callback function.")
(defun doi-utils-redirect-callback (&optional status)
"Callback for `url-retrieve' to set the redirect.
Optional argument STATUS Unknown why this is optional."
(when (plist-get status :error)
(signal (car (plist-get status :error)) (cdr(plist-get status :error))))
(when (plist-get status :redirect) ; is nil if there none
(setq *doi-utils-redirect* (plist-get status :redirect)))
;; we have done our job, so we are not waiting any more.
(setq *doi-utils-waiting* nil))
;; To actually get the redirect we use url-retrieve like this.
(defun doi-utils-get-redirect (doi)
"Get redirect url from `doi-utils-dx-doi-org-url'/doi."
;; we are going to wait until the url-retrieve is done
(setq *doi-utils-waiting* t)
;; start with no redirect. it will be set in the callback.
(setq *doi-utils-redirect* nil)
(url-retrieve
(format "%s%s" doi-utils-dx-doi-org-url doi)
'doi-utils-redirect-callback)
;; I suspect we need to wait here for the asynchronous process to
;; finish. we loop and sleep until the callback says it is done via
;; `*doi-utils-waiting*'. this works as far as i can tell. Before I
;; had to run this a few times to get it to work, which i suspect
;; just gave the first one enough time to finish.
(while *doi-utils-waiting* (sleep-for 0.1)))
;; Once we have a redirect for a particular doi, we need to compute the url to
;; the pdf. We do this with a series of functions. Each function takes a single
;; argument, the redirect url. If it knows how to compute the pdf url it does,
;; and returns it. We store the functions in a variable:
(defvar doi-utils-pdf-url-functions nil
"Functions that return a url to a pdf from a redirect url.
Each function takes one argument, the redirect url. The function
must return a pdf-url, or nil.")
;;** APS journals
(defun aps-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s*\\)://journals.aps.org" *doi-utils-redirect*)
(replace-regexp-in-string "/abstract/" "/pdf/" *doi-utils-redirect*)))
;;** Science
(defun science-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://www.sciencemag.org" *doi-utils-redirect*)
(concat *doi-utils-redirect* ".full.pdf")))
;;** Nature
(defun nature-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://www.nature.com" *doi-utils-redirect*)
(concat *doi-utils-redirect* ".pdf")))
;;** Elsevier/ScienceDirect
;; You cannot compute these pdf links; they are embedded in the redirected pages.
(defvar *doi-utils-pdf-url* nil
"Stores url to pdf download from a callback function.")
;;** Wiley
;; Wiley have changed the url structure from
;; http://onlinelibrary.wiley.com/doi/10.1002/anie.201402680/abstract
;; http://onlinelibrary.wiley.com/doi/10.1002/anie.201402680/pdf
;; to
;; http://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201402680
;; http://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.201402680
;; Hence fewer steps are now required.
;; https://onlinelibrary.wiley.com/doi/10.1002/adts.202200926
;; https://onlinelibrary.wiley.com/doi/epdf/10.1002/adts.202200926
;; (defun wiley-pdf-url (*doi-utils-redirect*)
;; "Get url to the pdf from *DOI-UTILS-REDIRECT*."
;; (when (string-match "^http\\(s?\\)://onlinelibrary.wiley.com" *doi-utils-redirect*)
;; (replace-regexp-in-string "doi/abs" "doi/pdf" *doi-utils-redirect*)))
(defun wiley-pdf-url-2 (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*.
[2023-04-10 Mon] updated a new rule.
https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/anie.201310461?download=true"
(when (string-match "^http\\(s?\\)://onlinelibrary.wiley.com" *doi-utils-redirect*)
(concat
(replace-regexp-in-string "doi/" "doi/pdfdirect/" *doi-utils-redirect*)
"?download=true")))
(defun agu-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "https://agupubs.onlinelibrary.wiley.com"
*doi-utils-redirect*)
(replace-regexp-in-string "/full/" "/pdfdirect/" *doi-utils-redirect*)))
;;** Springer
(defun springer-chapter-pdf-url (*doi-utils-redirect*)
(when (string-match "^http\\(s?\\)://link.springer.com/chapter/" *doi-utils-redirect*)
(replace-regexp-in-string "/chapter" "/content/pdf"
(concat *doi-utils-redirect* ".pdf"))))
(defun springer-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://link.springer.com" *doi-utils-redirect*)
(replace-regexp-in-string "/article/" "/content/pdf/"
(concat *doi-utils-redirect* ".pdf"))))
;;** ACS
;; here is a typical url http://pubs.acs.org/doi/abs/10.1021/nl500037x
;; the pdf is found at http://pubs.acs.org/doi/pdf/10.1021/nl500037x
;; we just change /abs/ to /pdf/.
(defun acs-pdf-url-1 (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://pubs.acs.org/doi/abs/" *doi-utils-redirect*)
(replace-regexp-in-string "/abs/" "/pdf/" *doi-utils-redirect*)))
;; 1/20/2016 I noticed this new pattern in pdf urls, where there is no abs in
;; the url
(defun acs-pdf-url-2 (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://pubs.acs.org/doi/" *doi-utils-redirect*)
(replace-regexp-in-string "/doi/" "/doi/pdf/" *doi-utils-redirect*)))
;; 1/18/2019: It looks like they are using https now
(defun acs-pdf-url-3 (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^https://pubs.acs.org/doi/" *doi-utils-redirect*)
(replace-regexp-in-string "/doi/" "/doi/pdf/" *doi-utils-redirect*)))
;;** IOP
(defun iop-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://iopscience.iop.org" *doi-utils-redirect*)
(concat *doi-utils-redirect* "/pdf")))
;;** JSTOR
(defun jstor-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://www.jstor.org" *doi-utils-redirect*)
(concat (replace-regexp-in-string "/stable/" "/stable/pdfplus/" *doi-utils-redirect*) ".pdf")))
;;** AIP
(defun aip-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://scitation.aip.org" *doi-utils-redirect*)
;; get stuff after content
(let (p1 p2 s p3)
(setq p2 (replace-regexp-in-string
"^http\\(s?\\)://scitation.aip.org/" "" *doi-utils-redirect*))
(setq s (split-string p2 "/"))
(setq p1 (mapconcat 'identity (org-ref--remove-at-indices '(0 6) s) "/"))
(setq p3 (concat "/" (nth 0 s) (nth 1 s) "/" (nth 2 s) "/" (nth 3 s)))
(format "http://scitation.aip.org/deliver/fulltext/%s.pdf?itemId=/%s&mimeType=pdf&containerItemId=%s"
p1 p2 p3))))
(defun aip-pdf-url-2 (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
;; [2021-08-28 Sat] Seems like they changed the link a little?
;; https://aip.scitation.org/doi/10.1063/1.5019667
;; to
;; https://aip.scitation.org/doi/pdf/10.1063/1.5019667
(when (string-match "^http\\(s?\\)://aip.scitation.org" *doi-utils-redirect*)
(concat "https://aip.scitation.org/doi/pdf" (cl-second (split-string *doi-utils-redirect* "doi")))))
;;** Taylor and Francis
(defun tandfonline-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://www.tandfonline.com" *doi-utils-redirect*)
(replace-regexp-in-string "/abs/\\|/full/" "/pdf/" *doi-utils-redirect*)))
;;** ECS
(defun ecs-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://jes.ecsdl.org" *doi-utils-redirect*)
(replace-regexp-in-string "\\.abstract$" ".full.pdf" *doi-utils-redirect*)))
;; http://ecst.ecsdl.org/content/25/2/2769
;; http://ecst.ecsdl.org/content/25/2/2769.full.pdf
(defun ecst-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://ecst.ecsdl.org" *doi-utils-redirect*)
(concat *doi-utils-redirect* ".full.pdf")))
;;** RSC
(defun rsc-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://pubs.rsc.org" *doi-utils-redirect*)
(let ((url (downcase *doi-utils-redirect*)))
(setq url (replace-regexp-in-string "articlelanding" "articlepdf" url))
url)))
;;** Science Direct
;; https://www.sciencedirect.com/science/article/pii/S001085452200577X?via%3Dihub
;; https://www.sciencedirect.com/science/article/pii/S001085452200577X/pdfft?isDTMRedir=true&download=true
(defun science-direct-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://www.sciencedirect.com" *doi-utils-redirect*)
(replace-string "?via%3Dihub" "/pdfft?isDTMRedir=true&download=true" *doi-utils-redirect*)))
;; (defun doi-utils-get-science-direct-pdf-url (redirect-url)
;; "Science direct hides the pdf url in html. We get it out here.
;; REDIRECT-URL is where the pdf url will be in."
;; (let ((first-url
;; (with-current-buffer (url-retrieve-synchronously redirect-url)
;; (goto-char (point-min))
;; (when (re-search-forward "pdf_url\" content=\"\\([^\"]*\\)\"" nil t)
;; (match-string-no-properties 1)))))
;; (and first-url
;; (with-current-buffer (url-retrieve-synchronously first-url)
;; (goto-char (point-min))
;; (when (re-search-forward "or click <a href=\"\\([^\"]*\\)\">" nil t)
;; (match-string-no-properties 1))))))
;; (defun science-direct-pdf-url (*doi-utils-redirect*)
;; "Get url to the pdf from *DOI-UTILS-REDIRECT*."
;; (when (string-match "^http\\(s?\\)://www.sciencedirect.com" *doi-utils-redirect*)
;; (doi-utils-get-science-direct-pdf-url *doi-utils-redirect*)))
;; sometimes I get
;; http://linkinghub.elsevier.com/retrieve/pii/S0927025609004558
;; which actually redirect to
;; http://www.sciencedirect.com/science/article/pii/S0927025609004558
;; https://www.sciencedirect.com/science/article/pii/S001085452200577X?via%3Dihub
;; https://www.sciencedirect.com/science/article/pii/S001085452200577X/pdfft?isDTMRedir=true&download=true
;; (defun linkinghub-elsevier-pdf-url (*doi-utils-redirect*)
;; "Get url to the pdf from *DOI-UTILS-REDIRECT*."
;; (when (string-match
;; "^https://linkinghub.elsevier.com/retrieve" *doi-utils-redirect*)
;; (science-direct-pdf-url
;; (replace-regexp-in-string
;; ;; change URL to science direct and use function to get pdf URL
;; "https://linkinghub.elsevier.com/retrieve"
;; "https://www.sciencedirect.com/science/article"
;; *doi-utils-redirect*))))
;; https://www.sciencedirect.com/science/article/pii/S1385894723014973/pdfft?isDTMRedir=true&download=true
(defun linkinghub-elsevier-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match
"^https://linkinghub.elsevier.com/retrieve" *doi-utils-redirect*)
(concat
(replace-regexp-in-string
;; change URL to science direct and use function to get pdf URL
"https://linkinghub.elsevier.com/retrieve"
"https://www.sciencedirect.com/science/article"
*doi-utils-redirect*)
"/pdfft?isDTMRedir=true")))
;;** PNAS
;; http://www.pnas.org/content/early/2014/05/08/1319030111
;; http://www.pnas.org/content/early/2014/05/08/1319030111.full.pdf
;; with supporting info
;; http://www.pnas.org/content/early/2014/05/08/1319030111.full.pdf+html?with-ds=yes
(defun pnas-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://www.pnas.org" *doi-utils-redirect*)
(concat *doi-utils-redirect* ".full.pdf?with-ds=yes")))
;;** Copernicus Publications
(defvar copernicus-journal-urls '(
"^https://www.adv-geosci.net/"
"^https://www.adv-radio-sci.net/"
"^https://www.adv-sci-res.net/"
"^https://www.adv-stat-clim-meteorol-oceanogr.net/"
"^https://www.ann-geophys.net/"
"^https://www.arch-anim-breed.net/"
"^https://www.astra-proc.net/"
"^https://www.atmos-chem-phys.net/"
"^https://www.atmos-chem-phys-discuss.net/"
"^https://www.atmos-meas-tech.net/"
"^https://www.atmos-meas-tech-discuss.net/"
"^https://www.biogeosciences.net/"
"^https://www.biogeosciences-discuss.net/"
"^https://www.clim-past.net/recent_papers.html"
"^https://www.clim-past-discuss.net/"
"^https://www.drink-water-eng-sci.net/"
"^https://www.drink-water-eng-sci-discuss.net/"
"^https://www.eg-quaternary-sci-j.net/"
"^https://www.earth-surf-dynam.net/"
"^https://www.earth-surf-dynam-discuss.net/"
"^https://www.earth-syst-dynam.net/"
"^https://www.earth-syst-dynam-discuss.net/"
"^https://www.earth-syst-sci-data.net/"
"^https://www.earth-syst-sci-data-discuss.net/"
"^https://www.foss-rec.net/"
"^https://www.geogr-helv.net/"
"^https://www.geosci-instrum-method-data-syst.net/"
"^https://www.geosci-instrum-method-data-syst-discuss.net/"
"^https://www.geosci-model-dev.net/"
"^https://www.geosci-model-dev-discuss.net/"
"^https://www.hist-geo-space-sci.net/"
"^https://www.hydrol-earth-syst-sci.net/"
"^https://www.hydrol-earth-syst-sci-discuss.net/"
"^https://www.j-sens-sens-syst.net/"
"^https://www.mech-sci.net/"
"^https://www.nat-hazards-earth-syst-sci.net/"
"^https://www.nonlin-processes-geophys-discuss.net/"
"^https://www.ocean-sci.net/"
"^https://www.ocean-sci-discuss.net/"
"^https://www.primate-biol.net/"
"^https://www.proc-iahs.net/"
"^https://www.sci-dril.net/"
"^https://www.soil-journal.net/"
"^https://www.soil-discuss.net/"
"^https://www.solid-earth.net/"
"^https://www.solid-earth-discuss.net/"
"^https://www.stephan-mueller-spec-publ-ser.net/"
"^https://www.the-cryosphere.net/"
"^https://www.the-cryosphere-discuss.net/"
"^https://www.web-ecol.net/"
"^https://www.wind-energ-sci.net/"
"^https://www.wind-energ-sci-discuss.net/"
)
"List of Copernicus URLs.")
(defun doi-utils-get-copernicus-pdf-url (redirect-url)
"Copernicus hides the pdf url in html. We get it out here.
REDIRECT-URL is where the pdf url will be in."
(setq *doi-utils-waiting* t)
(url-retrieve
redirect-url
(lambda (status)
(goto-char (point-min))
(re-search-forward "citation_pdf_url\" content=\"\\([^\"]*\\)\"" nil t)
(setq *doi-utils-pdf-url* (match-string 1)
*doi-utils-waiting* nil)))
(while *doi-utils-waiting* (sleep-for 0.1))
*doi-utils-pdf-url*)
(defun copernicus-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(car (cl-loop for copurl in copernicus-journal-urls
when (string-match copurl *doi-utils-redirect*)
collect
(progn (doi-utils-get-copernicus-pdf-url *doi-utils-redirect*)
*doi-utils-pdf-url*))))
;;** Sage
(defun sage-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://pss.sagepub.com" *doi-utils-redirect*)
(concat *doi-utils-redirect* ".full.pdf")))
;;** Journal of Neuroscience
(defun jneurosci-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://www.jneurosci.org" *doi-utils-redirect*)
(concat *doi-utils-redirect* ".full.pdf")))
;;** Generic .full.pdf
(defun generic-full-pdf-url (*doi-utils-redirect*)
(let ((pdf (concat *doi-utils-redirect* ".full.pdf")))
(when (url-http-file-exists-p pdf)
pdf)))
;;** IEEE
;; 10.1109/re.2014.6912247
;; http(s)://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6912247
;; http(s)://ieeexplore.ieee.org/ielx7/6903646/6912234/06912247.pdf
;; http(s)://ieeexplore.ieee.org/iel7/6903646/6912234/06912247.pdf?arnumber=6912247
;; <meta name="citation_pdf_url" content="http(s)://ieeexplore.ieee.org/iel7/6903646/6912234/06912247.pdf?arnumber=6912247">
;; <frame src="http(s)://ieeexplore.ieee.org/ielx7/6903646/6912234/06912247.pdf?tp=&arnumber=6912247&isnumber=6912234" frameborder=0 />
(defun ieee-pdf-url (*doi-utils-redirect*)
"Get a url to the pdf from *DOI-UTILS-REDIRECT* for IEEE urls."
(when (string-match "^https?://ieeexplore.ieee.org" *doi-utils-redirect*)
(with-current-buffer (url-retrieve-synchronously *doi-utils-redirect*)
(goto-char (point-min))
(when (re-search-forward "<meta name=\"citation_pdf_url\" content=\"\\([[:ascii:]]*?\\)\">" nil t)
(let ((framed-url (match-string 1)))
(with-current-buffer (url-retrieve-synchronously framed-url)
(goto-char (point-min))
(when (re-search-forward "<frame src=\"\\(http[[:ascii:]]*?\\)\"" nil t)
(match-string 1))))))))
;; At least some IEEE papers need the following new pdf-link parsing
;; Example: 10.1109/35.667413
(defun ieee2-pdf-url (*doi-utils-redirect*)
"Get a url to the pdf from *DOI-UTILS-REDIRECT* for IEEE urls."
(when (string-match "^https?://ieeexplore.ieee.org" *doi-utils-redirect*)
(with-current-buffer (url-retrieve-synchronously *doi-utils-redirect*)
(goto-char (point-min))
(when (re-search-forward "\"pdfUrl\":\"\\([[:ascii:]]*?\\)\"" nil t)
(let ((framed-url (match-string 1)))
(with-current-buffer (url-retrieve-synchronously (concat "http://ieeexplore.ieee.org" framed-url))
(goto-char (point-min))
(when (re-search-forward "<frame src=\"\\(http[[:ascii:]]*?\\)\"" nil t)
(match-string 1))))))))
;; Another try to get the ieee pdf
;; <iframe src="http(s)://ieeexplore.ieee.org/ielx5/8/4538127/04538164.pdf?tp=&arnumber=4538164&isnumber=4538127" frameborder=0>
(defun ieee3-pdf-url (*doi-utils-redirect*)
"Get a url to the pdf from *DOI-UTILS-REDIRECT* for IEEE urls."
(when (string-match "^https?://ieeexplore.ieee.org" *doi-utils-redirect*)
(with-current-buffer (url-retrieve-synchronously *doi-utils-redirect*)
(goto-char (point-min))
(when (re-search-forward "\"pdfUrl\":\"\\([[:ascii:]]*?\\)\"" nil t)
(let ((framed-url (match-string 1)))
(with-current-buffer (url-retrieve-synchronously (concat "http://ieeexplore.ieee.org" framed-url))
(goto-char (point-min))
(when (re-search-forward "<iframe src=\"\\(http[[:ascii:]]*?\\)\"" nil t)
(match-string 1))))))))
;; ACM Digital Library
;; https://dl.acm.org/doi/10.1145/1368088.1368132
(defun acm-pdf-url (*doi-utils-redirect*)
"Get a url to the pdf from *DOI-UTILS-REDIRECT* for ACM urls."
(when (string-match "^https?://dl.acm.org" *doi-utils-redirect*)
(replace-regexp-in-string "doi" "doi/pdf" *doi-utils-redirect* )))
;;** Optical Society of America (OSA)
(defun osa-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^https://www.osapublishing.org" *doi-utils-redirect*)
(replace-regexp-in-string "abstract.cfm" "viewmedia.cfm" *doi-utils-redirect* )))
;;** Publishers using Highwire Press metatags
;; For context and details, see:
;; https://webmasters.stackexchange.com/questions/72746/where-are-the-complete-set-of-highwire-press-metatags-defined
(defun highwire-pdf-url (*doi-utils-redirect*)
"Typical URL: http://biomechanical.asmedigitalcollection.asme.org/article.aspx?articleid=1427237
On this page the pdf might be here: <meta name=\"citation_author\" content=\"Dalong Li\" /><meta name=\"citation_author_email\" content=\"dal40@pitt.edu\" /><meta name=\"citation_author\" content=\"Anne M. Robertson\" /><meta name=\"citation_author_email\" content=\"rbertson@pitt.edu\" /><meta name=\"citation_title\" content=\"A Structural Multi-Mechanism Damage Model for Cerebral Arterial Tissue\" /><meta name=\"citation_firstpage\" content=\"101013\" /><meta name=\"citation_doi\" content=\"10.1115/1.3202559\" /><meta name=\"citation_keyword\" content=\"Mechanisms\" /><meta name=\"citation_keyword\" content=\"Biological tissues\" /><meta name=\"citation_keyword\" content=\"Stress\" /><meta name=\"citation_keyword\" content=\"Fibers\" /><meta name=\"citation_journal_title\" content=\"Journal of Biomechanical Engineering\" /><meta name=\"citation_journal_abbrev\" content=\"J Biomech Eng\" /><meta name=\"citation_volume\" content=\"131\" /><meta name=\"citation_issue\" content=\"10\" /><meta name=\"citation_publication_date\" content=\"2009/10/01\" /><meta name=\"citation_issn\" content=\"0148-0731\" /><meta name=\"citation_publisher\" content=\"American Society of Mechanical Engineers\" /><meta name=\"citation_pdf_url\" content=\"http://biomechanical.asmedigitalcollection.asme.org/data/journals/jbendy/27048/101013_1.pdf\" />
It is in the citation_pdf_url.
It would be better to parse this, but here I just use a regexp.
"
(when (or (string-match "^http\\(s?\\)://biomechanical.asmedigitalcollection.asme.org" *doi-utils-redirect*)
(string-match "^http\\(s?\\)://ojs.aaai.org" *doi-utils-redirect*)
(string-match "^http\\(s?\\)://aclanthology.org" *doi-utils-redirect*))
(setq *doi-utils-waiting* 0)
(url-retrieve
*doi-utils-redirect*
(lambda (status)
(or (progn (goto-char (point-min))
(re-search-forward "citation_pdf_url\"? content=\"\\(.*\\)\"" nil t))
(progn (goto-char (point-min))
(re-search-forward "\"\\([^\"]*\\)\" name=\"?citation_pdf_url" nil t)))
;; (message-box (match-string 1))
(setq *doi-utils-pdf-url* (match-string 1)
*doi-utils-waiting* nil)))
(while (and *doi-utils-waiting* (< *doi-utils-waiting* 5))
(setq *doi-utils-waiting* (+ *doi-utils-waiting* 0.1))
(sleep-for 0.1))
*doi-utils-pdf-url*))
;; Society for Industrial and Applied Mathematics (SIAM)
(defun siam-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s?\\)://epubs.siam.org" *doi-utils-redirect*)
(replace-regexp-in-string "/doi/" "/doi/pdf/" *doi-utils-redirect* )))
;; PLOS journals
;; https://plos.org/
(defun plos-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http\\(s*\\)://journals.plos.org" *doi-utils-redirect*)
(concat (replace-regexp-in-string (regexp-quote "/article?id=") "/article/file?id=" *doi-utils-redirect*) "&type=printable")))
;; https://www.frontiersin.org/articles/10.3389/fchem.2022.1037997/full
;; https://www.frontiersin.org/articles/10.3389/fchem.2022.1037997/pdf
(defun frontiers-pdf-url (*doi-utils-redirect*)
(when (string-match "^http\\(s*\\)://www.frontiersin.org" *doi-utils-redirect*)
(replace-regexp-in-string "/full" "/pdf" *doi-utils-redirect*)))
;; https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/celc.201902035
;; https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/celc.201902035
(defun chemistry-europe-pdf-url (*doi-utils-redirect*)
(when (string-match "^http\\(s*\\)://chemistry-europe.onlinelibrary.wiley.com" *doi-utils-redirect*)
(concat
(replace-regexp-in-string "/doi" "/doi/pdfdirect" *doi-utils-redirect*)
"?download=true")))
;; ** from issue #1081
(defun arxiv-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match-p "^https?://arxiv\\.org" *doi-utils-redirect*)
(concat (replace-regexp-in-string "/abs/" "/pdf/" *doi-utils-redirect*)
".pdf")))
(defun rss-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match-p "roboticsproceedings" *doi-utils-redirect*)
(concat (replace-regexp-in-string "\\.html" ".pdf" *doi-utils-redirect*))))
(defun ieeestamp-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^https?://ieeexplore\\.ieee\\.org/document/\\([0-9]+\\)"
*doi-utils-redirect*)
(concat "https://ieeexplore.ieee.org/stampPDF/getPDF.jsp?tp=&arnumber="
(match-string 1 *doi-utils-redirect*))))
;;** Add all functions
(setq doi-utils-pdf-url-functions
(list
'aps-pdf-url
'science-pdf-url
'nature-pdf-url
;; 'wiley-pdf-url
'wiley-pdf-url-2
'springer-chapter-pdf-url
'springer-pdf-url
'acs-pdf-url-1
'acs-pdf-url-2
'acs-pdf-url-3
'iop-pdf-url
'jstor-pdf-url
'aip-pdf-url
'aip-pdf-url-2
'science-direct-pdf-url
'linkinghub-elsevier-pdf-url
'tandfonline-pdf-url
'ecs-pdf-url
'ecst-pdf-url
'rsc-pdf-url
'pnas-pdf-url
'copernicus-pdf-url
'sage-pdf-url
'jneurosci-pdf-url
'ieee-pdf-url
'ieee2-pdf-url
'ieee3-pdf-url
'acm-pdf-url
'osa-pdf-url
'highwire-pdf-url
'siam-pdf-url
'agu-pdf-url
'plos-pdf-url
'frontiers-pdf-url
'chemistry-europe-pdf-url
'generic-full-pdf-url
'arxiv-pdf-url
'rss-pdf-url
'ieeestamp-pdf-url))
;;** Get the pdf url for a doi
(defun doi-utils-get-pdf-url (doi)
"Return a url to a pdf for the DOI if one can be calculated.
Loops through the functions in `doi-utils-pdf-url-functions'
until one is found."
(doi-utils-get-redirect doi)
(unless *doi-utils-redirect*
(error "No redirect found for %s" doi))
(catch 'pdf-url
(dolist (func doi-utils-pdf-url-functions)
(let ((this-pdf-url (funcall func *doi-utils-redirect*)))
(when this-pdf-url
(throw 'pdf-url this-pdf-url))))))
;;** Finally, download the pdf
(defvar bibtex-completion-library-path)
(defvar bibtex-completion-bibliography)
(declare-function async-start "async")
;;;###autoload
(defun doi-utils-async-download-pdf ()
"Download the PDF for bibtex entry at point asynchronously.
It is not fully async, only the download is. Fully async is
harder because you need to run `doi-utils-get-pdf-url' async
too. "
(interactive)
(require 'async)
(save-excursion
(bibtex-beginning-of-entry)
(let (;; get doi, removing http://dx.doi.org/ if it is there.
(doi (replace-regexp-in-string
"https?://\\(dx.\\)?.doi.org/" ""
(bibtex-autokey-get-field "doi")))
(base-name (funcall doi-utils-pdf-filename-function))
(pdf-url)
(pdf-file))
(setq pdf-file
(concat (cond
((stringp bibtex-completion-library-path)
bibtex-completion-library-path)
((= 1 (length bibtex-completion-library-path))
(car bibtex-completion-library-path))
(t
(completing-read "Dir: " bibtex-completion-library-path)))
base-name ".pdf"))
(unless doi (error "No DOI found to get a pdf for"))
(when (file-exists-p pdf-file)
(error "%s already exists. Delete to re-download" pdf-file))
;; (doi-utils-get-pdf-url "10.1063/1.5019667")
;; If you get here, try getting the pdf file
(async-start
`(lambda ()
(setq package-user-dir ,package-user-dir)
(require 'package)
(package-initialize)
(setq load-path (list ,@load-path))
(require 'doi-utils)
(setq pdf-url (doi-utils-get-pdf-url ,doi))
(when pdf-url
(url-copy-file pdf-url ,pdf-file t)
(let* ((header (with-temp-buffer
(set-buffer-multibyte nil)
(insert-file-contents-literally ,pdf-file nil 0 5)
(buffer-string)))
(valid (and (stringp header)
(string-equal (encode-coding-string header 'utf-8) "%PDF-"))))
(if valid
(format "%s downloaded" ,pdf-file)
(delete-file ,pdf-file)
(require 'browse-url)
(browse-url pdf-url)
(message "Invalid pdf (file deleted). Header = %s" header)))))
`(lambda (result)
(message "doi-utils-async-download-pdf: %s" result))))))
;;;###autoload
(defun doi-utils-get-bibtex-entry-pdf (&optional arg)
"Download pdf for entry at point if the pdf does not already exist locally.
The entry must have a doi. The pdf will be saved, by the name
%s.pdf where %s is the bibtex label. Files will not be
overwritten. The pdf will be checked to make sure it is a pdf,
and not some html failure page. You must have permission to
access the pdf. We open the pdf at the end if
`doi-utils-open-pdf-after-download' is non-nil.
With one prefix ARG, directly get the pdf from a file (through
`read-file-name') instead of looking up a DOI. With a double
prefix ARG, directly get the pdf from an open buffer (through
`read-buffer-to-switch') instead. These two alternative methods
work even if the entry has no DOI, and the pdf file is not
checked."
(interactive "P")
(save-excursion
(bibtex-beginning-of-entry)
(let (;; get doi, removing http://dx.doi.org/ if it is there.
(doi (replace-regexp-in-string
"https?://\\(dx.\\)?.doi.org/" ""
(bibtex-autokey-get-field "doi")))
(base-name (funcall doi-utils-pdf-filename-function))
(pdf-url)
(pdf-file))
(setq pdf-file
(concat (cond
((stringp bibtex-completion-library-path)
bibtex-completion-library-path)
((= 1 (length bibtex-completion-library-path))
(car bibtex-completion-library-path))
(t
(completing-read "Dir: " bibtex-completion-library-path)))
base-name ".pdf"))
;; now get file if needed.
(unless (file-exists-p pdf-file)
(cond
((and (not arg)
doi
(setq pdf-url (doi-utils-get-pdf-url doi)))
(url-copy-file pdf-url pdf-file)
;; now check if we got a pdf
(if (org-ref-pdf-p pdf-file)
(message "%s saved" pdf-file)
(delete-file pdf-file)
(message "No pdf was downloaded.")
(browse-url pdf-url)))
((equal arg '(4))
(copy-file (expand-file-name (read-file-name "Pdf file: " nil nil t))
pdf-file))
((equal arg '(16))
(with-current-buffer (read-buffer-to-switch "Pdf buffer: ")
(write-file pdf-file)))
(t
(message "We don't have a recipe for this journal.")))
(when (file-exists-p pdf-file)
(bibtex-set-field "file" pdf-file))
(when (and doi-utils-open-pdf-after-download (file-exists-p pdf-file))
(org-open-file pdf-file))))))
;;* Getting bibtex entries from a DOI
;; [[http://homepages.see.leeds.ac.uk/~eeaol/notes/2013/02/doi-metadata/][found]]
;; you can download metadata about a DOI from http://dx.doi.org. You just have
;; to construct the right http request to get it. Here is a function that gets
;; the metadata as a plist in emacs.
;;
;;
(defvar doi-utils-cache nil
"Cache variable for storing data we can reuse.
A-list (doi . data) where doi is doi string, and data is what is
retrieved from it. This is transient, and disappears when you
restart Emacs. This mostly exists to prevent
`doi-utils-update-field' from needing to download the data for
every field.")
(defun doi-utils-clear-cache ()
"Clear `doi-utils-cache'."
(interactive)
(setq doi-utils-cache '()))
(defun doi-utils-get-json-metadata (doi)
"Try to get json metadata for DOI. Open the DOI in a browser if we do not get it."
(if-let* ((data (cdr (assoc doi doi-utils-cache))))
;; We have the data already, so we return it.
data
(let ((url-request-method "GET")
(url-mime-accept-string "application/citeproc+json")
(json-object-type 'plist)
(json-data)
(url (concat doi-utils-dx-doi-org-url doi)))
(with-temp-buffer
(url-insert
(url-retrieve-synchronously url))
(setq json-data (buffer-string))
(when (or (string-match "<title>Error: DOI Not Found</title>" json-data)
(string-match "Resource not found" json-data)
(string-match "Status *406" json-data)
(string-match "400 Bad Request" json-data))
(browse-url (concat doi-utils-dx-doi-org-url doi))
(error "Something went wrong. We got this response:
%s
Opening %s" json-data url))
(setq data (json-read-from-string json-data))
(cl-pushnew (cons doi data) doi-utils-cache)
data))))
(defun doi-utils-get-json-metadata-curl (doi)
"Try to get json metadata for DOI. Open the DOI in a browser if we do not get it."
(let ((json-object-type 'plist)
(json-data)
(url (concat doi-utils-dx-doi-org-url doi)))
(with-temp-buffer
(call-process "curl" nil t nil
"--location"
"--silent"
"--header"
"Accept: application/citeproc+json"
url)
(setq json-data (buffer-string))
(cond
((or (string-match "<title>Error: DOI Not Found</title>" json-data)
(string-match "Resource not found" json-data)
(string-match "Status *406" json-data)
(string-match "400 Bad Request" json-data))
(browse-url url)
(error "Something went wrong. We got this response:
%s
Opening %s" json-data url))
;; everything seems ok with the data
(t
(json-read-from-string json-data))))))
;; We can use that data to construct a bibtex entry. We do that by defining a
;; template, and filling it in. I wrote this template expansion code which
;; makes it easy to substitute values like %{} in emacs lisp.
(defun doi-utils-expand-template (s)
"Expand a string template S containing %{} with the eval of its contents."
(replace-regexp-in-string "%{\\([^}]+\\)}"
(lambda (arg)
(let ((sexp (substring arg 2 -1)))
(format "%s" (eval (read sexp)))))
s))
;; Now we define a function that fills in that template from the metadata.
;; As different bibtex types share common keys, it is advantageous to separate
;; data extraction from json, and the formatting of the bibtex entry.
;; We use eval-and-compile because we use the three following forms in the
;; `doi-utils-def-bibtex-type' macro. Since the macro is expanded at compile
;; time, we need to ensure these defuns and defvars are evaluated at
;; compile-time.
(eval-and-compile
(defvar doi-utils-json-metadata-extract
'((type (plist-get results :type))
(author (mapconcat (lambda (x)
(message "%s" x)
(if (plist-get x :name)
(plist-get x :name)
(concat (plist-get x :given) " " (plist-get x :family))))
(plist-get results :author) " and "))
(title (plist-get results :title))
(subtitle (plist-get results :subtitle))
(journal (plist-get results :container-title))
(series (plist-get results :container-title))
(publisher (plist-get results :publisher))
(volume (plist-get results :volume))
(issue (plist-get results :issue))
(number (plist-get results :issue))
(year (or (elt (elt (plist-get (plist-get results :issued) :date-parts) 0) 0)
(elt (elt (plist-get (plist-get results :approved) :date-parts) 0) 0)
))
;; Some dates don't have a month in them.
(month (let ((date (elt
(plist-get (plist-get results :issued) :date-parts) 0)))
(if (>= (length date) 2)
(elt date 1)
"-")))
(pages (or (plist-get results :page)
(plist-get results :article-number)))
(doi (plist-get results :DOI))
(url (plist-get results :URL))
(booktitle (plist-get results :container-title))
(school (or (plist-get results :school)
(plist-get (plist-get results :institution) :name)))
;; I am not sure how general this is. This gets the first name.
(institution (plist-get (car (plist-get results :institution)) :name))))
;; Next, we need to define the different bibtex types. Each type has a bibtex
;; type (for output) and the type as provided in the doi record. Finally, we
;; have to declare the fields we want to output.
(defvar doi-utils-bibtex-type-generators nil)
(defun doi-utils-concat-prepare (lst &optional acc)
"Minimize the number of args passed to `concat' from LST.
Given a list LST of strings and other expressions, which are
intended to be passed to `concat', concat any subsequent strings,
minimising the number of arguments being passed to `concat'
without changing the results. ACC is the list of additional
expressions."
(cond ((null lst) (nreverse acc))
((and (stringp (car lst))
(stringp (car acc)))
(doi-utils-concat-prepare (cdr lst) (cons (concat (car acc) (car lst))
(cdr acc))))
(t (doi-utils-concat-prepare (cdr lst) (cons (car lst) acc))))))
(defmacro doi-utils-def-bibtex-type (name matching-types &rest fields)
"Define a BibTeX type identified by (symbol) NAME.
MATCHING-TYPES is a list of strings. FIELDS are symbols that
match to retrieval expressions in
`doi-utils-json-metadata-extract'. This type will only be used
when the `:type' parameter in the JSON metadata is contained in
MATCHING-TYPES."
`(push (lambda (type results)
(when
(or ,@(mapcar
(lambda (match-type)
`(string= type ,match-type)) matching-types))
(let ,(mapcar (lambda (field)
(let ((field-expr
(assoc field doi-utils-json-metadata-extract)))
(if field-expr
;; need to convert to string first
`(,(car field-expr) (format "%s" ,(cadr field-expr)))
(error "Unknown bibtex field type %s" field))))
fields)
(concat
,@(doi-utils-concat-prepare
(org-ref--flatten-list
(list (concat "@" (symbol-name name) "{,\n")
;; there seems to be some bug with mapcan,
;; so we fall back to flatten
(mapcar (lambda (field)
`(" " ,(symbol-name field) " = {" ,field "},\n"))
fields)
"}\n")))))))
doi-utils-bibtex-type-generators))
(doi-utils-def-bibtex-type article ("journal-article" "article-journal" "article")
author title journal year volume number pages doi url)
(doi-utils-def-bibtex-type inproceedings ("proceedings-article" "paper-conference")
author title booktitle year month pages doi url)
(doi-utils-def-bibtex-type book ("book" "edited-book")
author title series publisher year pages doi url)
(doi-utils-def-bibtex-type inbook ("chapter" "book-chapter" "reference-entry")
author title booktitle series publisher year pages doi url)
(doi-utils-def-bibtex-type phdthesis ("phdthesis" "thesis" "dissertation")
author title school publisher year)
(doi-utils-def-bibtex-type techreport ("report")
institution author title publisher year doi url)
;; this is what preprints in chemrxiv look like for now
(doi-utils-def-bibtex-type misc ("posted-content")
author title year doi url)
;; With the code generating the bibtex entry in place, we can glue it to the json retrieval code.
(defun doi-utils-doi-to-bibtex-string (doi)
"Return a bibtex entry as a string for the DOI. Not all types are supported yet."
(let* ((results (funcall doi-utils-metadata-function doi))
(type (plist-get results :type)))
;; (format "%s" results) ; json-data
(or (cl-some (lambda (g) (funcall g type results)) doi-utils-bibtex-type-generators)
(message "%s not supported yet\n%S." type results))))
;; That is just the string for the entry. To be useful, we need a function that
;; inserts the string into a buffer. This function will insert the string at the
;; cursor, clean the entry, try to get the pdf.
(defun doi-utils-insert-bibtex-entry-from-doi (doi)
"Insert and clean bibtex entry from a DOI."
(insert (doi-utils-doi-to-bibtex-string doi))
(backward-char)
;; set date added for the record
(let ((ts (funcall doi-utils-timestamp-format-function)))
(when ts
(bibtex-set-field doi-utils-timestamp-field
ts)))
(org-ref-clean-bibtex-entry)
(when (buffer-file-name)
(save-buffer)))
;;;###autoload
(defun doi-utils-add-bibtex-entry-from-doi (doi &optional bibfile)
"Add DOI entry to end of a file in the current directory.
Pick the file ending with .bib or in . If you have an active region that
starts like a DOI, that will be the initial prompt. If no region
is selected and the first entry of the ‘kill-ring’ starts like a
DOI, then that is the initial prompt. Otherwise, you have to type
or paste in a DOI.
Argument BIBFILE the bibliography to use."
(interactive
(list (read-string
"DOI: "
;; now set initial input
(doi-utils-maybe-doi-from-region-or-current-kill))))
(unless bibfile
(setq bibfile (completing-read "Bibfile: " (org-ref-possible-bibfiles))))
;; Wrap in save-window-excursion to restore your window arrangement after this
;; is done.
(save-window-excursion
(with-current-buffer
(find-file-noselect bibfile)
;; Check if the doi already exists
(goto-char (point-min))
(if (re-search-forward (concat doi "\\_>") nil t)
(message "%s is already in this file" doi)
(goto-char (point-max))
(when (not (looking-back "\n\n" (min 3 (point))))
(insert "\n\n"))
(doi-utils-insert-bibtex-entry-from-doi doi)
(save-buffer)))))
(defalias 'doi-add-bibtex-entry 'doi-utils-add-bibtex-entry-from-doi
"Alias function for convenience.")
(defun doi-utils-maybe-doi-from-region-or-current-kill ()
"Try to get a DOI from the active region or current kill."
(let* ((the-active-region (if (region-active-p) ;; nil if no active region
(buffer-substring (region-beginning) (region-end))
nil))
(the-current-kill (ignore-errors (current-kill 0 t))) ;; nil if empty kill ring
;; DOI urls
;; Ex: https://doi.org/10.1109/MALWARE.2014.6999410
;; Ex: https://dx.doi.org/10.1007/978-3-319-60876-1_10
(doi-url-prefix-regexp "^https?://\\(dx\\.\\)?doi\\.org/")
;; https://www.crossref.org/blog/dois-and-matching-regular-expressions/
(doi-regexp "10\\.[0-9]\\{4,9\\}/[-._;()/:A-Z0-9]+$"))
(cond
;; Check if a DOI can be found in the active region
;; DOI raw
;; Ex: 10.1109/MALWARE.2014.6999410
((and (stringp the-active-region)
(org-ref--string-match (concat "^" doi-regexp) the-active-region))
the-active-region)
;; DOI url
;; Ex: https://doi.org/10.1109/MALWARE.2014.6999410
((and (stringp the-active-region)
(org-ref--string-match (concat doi-url-prefix-regexp doi-regexp) the-active-region))
(replace-regexp-in-string doi-url-prefix-regexp "" the-active-region))
;; DOI url as customized
((and (stringp the-active-region)
(org-ref--string-match (regexp-quote doi-utils-dx-doi-org-url) the-active-region))
(replace-regexp-in-string (regexp-quote doi-utils-dx-doi-org-url) "" the-active-region))
;; Check if DOI can be found in the current kill
;; DOI raw
;; Ex: 10.1109/MALWARE.2014.6999410
((and (stringp the-current-kill)
(org-ref--string-match (concat "^" doi-regexp) the-current-kill))
the-current-kill)
;; DOI url
;; Ex: https://doi.org/10.1109/MALWARE.2014.6999410
((and (stringp the-current-kill)
(org-ref--string-match (concat doi-url-prefix-regexp doi-regexp) the-current-kill))
(replace-regexp-in-string doi-url-prefix-regexp "" the-current-kill))
;; DOI url as customized
((and (stringp the-current-kill)
(org-ref--string-match (regexp-quote doi-utils-dx-doi-org-url) the-current-kill))
(replace-regexp-in-string (regexp-quote doi-utils-dx-doi-org-url) "" the-current-kill))
;; otherwise, return nil
(t
nil))))
;;;###autoload
(defun doi-utils-doi-to-org-bibtex (doi)
"Convert a DOI to an ‘org-bibtex’ form and insert it at point."
(interactive "sDOI: ")
(with-temp-buffer
(insert (doi-utils-doi-to-bibtex-string doi))
(bibtex-clean-entry)
(kill-region (point-min) (point-max)))
(org-bibtex-yank)
(org-metaright)
(org-metaright))
;;* Updating bibtex entries
;; I wrote this code because it is pretty common for me to copy bibtex entries
;; from ASAP articles that are incomplete, e.g. no page numbers because it is
;; not in print yet. I wanted a convenient way to update an entry from its DOI.
;; Basically, we get the metadata, and update the fields in the entry.
;; There is not bibtex set field function, so I wrote this one.
;;;###autoload
(defun bibtex-set-field (field value &optional nodelim)
"Set FIELD to VALUE in bibtex file. create field if it does not exist.
Optional argument NODELIM see `bibtex-make-field'."
(interactive "sfield: \nsvalue: ")
(bibtex-beginning-of-entry)
(let ((found))
(if (setq found (bibtex-search-forward-field field t))
;; we found a field
(progn
(goto-char (car (cdr found)))
(when value
(bibtex-kill-field)
(bibtex-make-field field nil nil nodelim)
(backward-char)
(insert value)))
;; make a new field
(bibtex-beginning-of-entry)
(forward-line) (beginning-of-line)
(bibtex-next-field nil)
(forward-char)
(bibtex-make-field field nil nil nodelim)
(backward-char)
(insert value))))
(defun plist-get-keys (plist)
"Return keys in a PLIST."
(cl-loop for (key _value) on plist by #'cddr collect key))
;;;###autoload
(defun doi-utils-update-bibtex-entry-from-doi (doi)
"Update fields in a bibtex entry from the DOI.
Every field will be updated, so previous change will be lost."
(interactive (list
(or (replace-regexp-in-string
"https?://\\(dx.\\)?doi.org/" ""
(bibtex-autokey-get-field "doi"))
(read-string "DOI: "))))
(let* ((results (funcall doi-utils-metadata-function doi))
(type (plist-get results :type))
(author (mapconcat
(lambda (x)
;; There are two possible ways an author is named. The most
;; common is with :given and :family, but sometimes there is
;; :name instead.
(if (plist-get x :name)
(plist-get x :name)
(concat (plist-get x :given)
" " (plist-get x :family))))
(plist-get results :author) " and "))
(title (plist-get results :title))
(journal (plist-get results :container-title))
(year (format "%s"
(elt
(elt
(plist-get
(plist-get results :issued) :date-parts) 0) 0)))
(volume (plist-get results :volume))
(number (or (plist-get results :issue) ""))
(pages (or (plist-get results :page) ""))
(url (or (plist-get results :URL) ""))
(doi (plist-get results :DOI))
mapping)
;; map the json fields to bibtex fields. The code each field is mapped to is
;; evaluated.
(setq mapping '((:author . (bibtex-set-field "author" author))
(:title . (bibtex-set-field "title" title))
(:container-title . (bibtex-set-field "journal" journal))
(:issued . (bibtex-set-field "year" year))
(:volume . (bibtex-set-field "volume" volume))
(:issue . (bibtex-set-field "number" number))
(:page . (bibtex-set-field "pages" pages))
(:DOI . (bibtex-set-field "doi" doi))
(:URL . (bibtex-set-field "url" url))))
;; now we have code to run for each entry. we map over them and evaluate the code
(mapc
(lambda (key)
(eval (cdr (assoc key mapping))))
(plist-get-keys results)))
(org-ref-clean-bibtex-entry))
;; A downside to updating an entry is it overwrites what you have already fixed.
;; So, we next develop a function to update the field at point.
;;;###autoload
(defun doi-utils-update-field ()
"Update the field at point in the bibtex entry.
Data is retrieved from the doi in the entry."
(interactive)
(let* ((doi (bibtex-autokey-get-field "doi"))
(results (funcall doi-utils-metadata-function doi))
(field (car (bibtex-find-text-internal nil nil ","))))
(cond
((string= field "volume")
(bibtex-set-field field (plist-get results :volume)))
((string= field "number")
(bibtex-set-field field (plist-get results :issue)))
((string= field "pages")
(bibtex-set-field field (or (plist-get results :page)
(plist-get results :article-number))))
((string= field "year")
(bibtex-set-field field (plist-get results :year)))
(t
(message "%s not supported yet." field)))))
;;* DOI functions for WOS
;; I came across this API http://wokinfo.com/media/pdf/OpenURL-guide.pdf to make
;; links to the things I am interested in here. Based on that document, here are
;; three links based on a doi:10.1021/jp047349j that take you to different Web
;; Of Science (WOS) pages.
;; 1. go to article in WOS: http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:doi/10.1021/jp047349j
;; 2. citing articles: http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info%3Adoi%2F10.1021/jp047349j&svc_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Asch_svc&svc.citing=yes
;; 3. related articles: http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info%3Adoi%2F10.1021/jp047349j&svc_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Asch_svc&svc.related=yes
;; These are pretty easy to construct, so we can write functions that will
;; create them and open the url in our browser. There are some other options
;; that could be considered, but since we usually have a doi, it seems like the
;; best way to go for creating the links. Here are the functions.
;;;###autoload
(defun doi-utils-wos (doi)
"Open Web of Science entry for DOI."
(interactive "sDOI: ")
(browse-url
(format
"http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:doi/%s" doi)))
;;;###autoload
(defun doi-utils-wos-citing (doi)
"Open Web of Science citing articles entry for DOI.
May be empty if none are found."
(interactive "sDOI: ")
(browse-url
(concat
"http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info%3Adoi%2F"
doi
"&svc_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Asch_svc&svc.citing=yes")))
;;;###autoload
(defun doi-utils-wos-related (doi)
"Open Web of Science related articles page for DOI."
(interactive "sDOI: ")
(browse-url
(concat "http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info%3Adoi%2F"
doi
"&svc_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Asch_svc&svc.related=yes")))
;;* DOI functions for ADS
;;;###autoload
(defun doi-utils-ads (doi)
"Open ADS entry for DOI"
(interactive "sDOI: ")
(browse-url
(concat
"https://ui.adsabs.harvard.edu/abs/" "%22" doi "%22")))
;;* A new doi link for org-mode
;; The idea is to add a menu to the doi link, so rather than just clicking to open the article, you can do other things.
;; 1. open doi
;; 2. open in wos
;; 3. open citing articles
;; 4. open related articles
;; 5. open bibtex entry
;; 6. get bibtex entry
;;;###autoload
(defun doi-utils-open (doi)
"Open DOI in browser."
(interactive "sDOI: ")
(browse-url (concat doi-utils-dx-doi-org-url doi)))
;;;###autoload
(defun doi-utils-open-bibtex (doi)
"Search through variable `bibtex-completion-bibliography' for DOI."
(interactive "sDOI: ")
(cl-loop for f in (org-ref-normalize-bibtex-completion-bibliography)
when (progn (find-file f)
(when (search-forward doi (point-max) t)
(bibtex-beginning-of-entry)))
return f))
;;;###autoload
(defun doi-utils-crossref (doi)
"Search DOI in CrossRef."
(interactive "sDOI: ")
(browse-url
(format
"http://search.crossref.org/?q=%s" doi)))
;;;###autoload
(defun doi-utils-google-scholar (doi)
"Google scholar the DOI."
(interactive "sDOI: ")
(browse-url
(format
"http://scholar.google.com/scholar?q=%s" doi)))
;;;###autoload
(defun doi-utils-pubmed (doi)
"Search Pubmed for the DOI."
(interactive "sDOI: ")
(browse-url
(format
"http://www.ncbi.nlm.nih.gov/pubmed/?term=%s"
(url-hexify-string doi))))
(declare-function org-element-property "org-element")
(defun doi-utils--context-doi ()
(org-element-property :path (org-element-context)))
(transient-define-prefix doi-link-follow-menu ()
"DOI actions."
[["Actions"
("o" "open" (lambda () (interactive)
(doi-utils-open (doi-utils--context-doi))))
("w" "wos" (lambda () (interactive)
(doi-utils-wos (doi-utils--context-doi))))
("c" "wos citing articles" (lambda () (interactive)
(doi-utils-wos-citing (doi-utils--context-doi))))
("r" "wos related articles" (lambda () (interactive)
(doi-utils-wos-related (doi-utils--context-doi))))
("a" "ads" (lambda () (interactive)
(doi-utils-ads (doi-utils--context-doi))))
("s" "Google Scholar" (lambda () (interactive)
(doi-utils-google-scholar (doi-utils--context-doi))))
("f" "CrossRef" (lambda () (interactive)
(doi-utils-crossref (doi-utils--context-doi))))
("p" "Pubmed" (lambda () (interactive)
(doi-utils-pubmed (doi-utils--context-doi))))
("b" "open in bibtex" (lambda () (interactive)
(doi-utils-open-bibtex (doi-utils--context-doi))))
("g" "get bibtex entry" (lambda () (interactive)
(doi-utils-add-bibtex-entry-from-doi (doi-utils--context-doi))))
("q" "quit" transient-quit-one)]])
(define-obsolete-function-alias 'doi-link-follow/body
#'doi-link-follow-menu "3.1")
(org-link-set-parameters "doi"
:follow (lambda (_) (doi-link-follow-menu))
:export (lambda (doi desc format)
(cond
((eq format 'html)
(format "<a href=\"%s%s\">%s</a>"
doi-utils-dx-doi-org-url
doi
(or desc (concat "doi:" doi))))
((eq format 'latex)
(format "\\href{%s%s}{%s}"
doi-utils-dx-doi-org-url
doi
(or desc (concat "doi:" doi)))))))
;;* Getting a doi for a bibtex entry missing one
;; Some bibtex entries do not have a DOI, maybe because they were entered by
;; hand, or copied from a source that did not have it available. Here we develop
;; some functions to help you find the DOI using Crossref.
;; Here is our example bibtex entry.
;; #+BEGIN_SRC bibtex
;; @article{deml-2014-oxide,
;; author = {Ann M. Deml and Vladan Stevanovi{\'c} and
;; Christopher L. Muhich and Charles B. Musgrave and
;; Ryan O'Hayre},
;; title = {Oxide Enthalpy of Formation and Band Gap Energy As
;; Accurate Descriptors of Oxygen Vacancy Formation
;; Energetics},
;; journal = {Energy Environ. Sci.},
;; volume = 7,
;; number = 6,
;; pages = 1996,
;; year = 2014,
;; doi = {10.1039/c3ee43874k,
;; url = {http://dx.doi.org/10.1039/c3ee43874k}},
;; }
;; The idea is to query Crossref in a way that is likely to give us a hit
;; relevant to the entry.
;; According to http://search.crossref.org/help/api we can send a query with a
;; free form citation that may give us something back. We do this to get a list
;; of candidates, which could be used to get the doi.
(declare-function org-ref-bib-citation "org-ref-bibtex")
;;;###autoload
(defun doi-utils-crossref-citation-query ()
"Query Crossref with the title of the bibtex entry at point.
Get a list of possible matches. Choose one with completion."
(interactive)
(bibtex-beginning-of-entry)
(let* ((entry (bibtex-parse-entry))
(raw-json-string)
(json-string)
(json-data)
(doi (bibtex-autokey-get-field "doi")))
(unless (string= "" doi)
(error "Entry already has a doi field"))
(with-current-buffer
(url-retrieve-synchronously
(concat
"http://search.crossref.org/dois?q="
(url-hexify-string (org-ref-bib-citation))))
(save-excursion
(goto-char (point-min))
(while (re-search-forward "<i>\\|</i>" nil t)
(replace-match ""))
(goto-char (point-min))
(while (re-search-forward "&amp;" nil t)
(replace-match "&"))
(goto-char (point-min))
(while (re-search-forward "&quot;" nil t)
(replace-match "\\\"" nil t)))
(setq raw-json-string (buffer-substring url-http-end-of-headers (point-max)))
;; decode json string
(setq json-string (decode-coding-string (encode-coding-string raw-json-string 'utf-8) 'utf-8))
(setq json-data (json-read-from-string json-string)))
(let* ((name (format "Crossref hits for %s" (org-ref-bib-citation)))
(candidates (mapcar (lambda (x)
(cons
(concat
(cdr (assoc 'fullCitation x)))
(cdr (assoc 'doi x))))
json-data))
(doi (cdr (assoc (completing-read "DOI: " candidates) candidates))))
(bibtex-make-field "doi" t)
(backward-char)
;; crossref returns doi url, but I prefer only a doi for the doi field
(insert (replace-regexp-in-string "^https?://\\(dx.\\)?doi.org/" "" doi))
(when (string= "" (bibtex-autokey-get-field "url"))
(bibtex-make-field "url" t)
(backward-char)
(insert doi)))))
;;* Debugging a DOI
;; I wrote this function to help debug a DOI. This function generates an
;; org-buffer with the doi, gets the json metadata, shows the bibtex entry, and
;; the pdf link for it.
(defun doi-utils-get-json (doi)
"Return json data as a string for DOI."
(let ((url-request-method "GET")
(url-mime-accept-string "application/citeproc+json")
(json-data))
(with-temp-buffer
(url-insert
(url-retrieve-synchronously
(concat doi-utils-dx-doi-org-url doi)))
(setq json-data (buffer-string))
(if (string-match "Resource not found" json-data)
(progn
(browse-url (concat doi-utils-dx-doi-org-url doi))
(error "Resource not found. Opening website"))
json-data))))
;;;###autoload
(defun doi-utils-debug (doi)
"Generate an org-buffer showing data about DOI."
(interactive "sDOI: ")
(switch-to-buffer "*debug-doi*")
(erase-buffer)
(org-mode)
(insert (concat "doi:" doi) "\n\n")
(insert "* JSON
"
(let ((url-request-method "GET")
(url-mime-accept-string "application/citeproc+json"))
(pp
(json-read-from-string (with-temp-buffer
(url-insert
(url-retrieve-synchronously
(concat doi-utils-dx-doi-org-url doi)))
(buffer-string)))))
"\n\n")
(goto-char (point-min)))
;;* Adding a bibtex entry from a crossref query
;; The idea here is to perform a query on Crossref, get a completion buffer of
;; candidates, and select the entry(ies) you want to add to your bibtex file.
;; You can select a region, e.g. a free form citation, or set of words, or you
;; can type the query in by hand.
;;;###autoload
(defun doi-utils-add-entry-from-crossref-query (query bibtex-file)
"Search Crossref with QUERY and use completion to select an entry to add to BIBTEX-FILE."
(interactive (list
(read-string
"Query: "
;; now set initial input
(cond
;; If region is active assume we want it
((region-active-p)
(replace-regexp-in-string
"\n" " "
(buffer-substring (region-beginning) (region-end))))
;; type or paste it in
(t
nil)))
(completing-read
"Bibfile: "
(append (org-ref--directory-files "." (lambda (f) (org-ref--file-ext-p f "bib")))
bibtex-completion-bibliography))))
(let* ((json-data (with-temp-buffer
(url-insert
(url-retrieve-synchronously
(concat
"https://api.crossref.org/works?query="
(url-hexify-string query))))
(json-read-from-string (buffer-string))))
(name (format "Crossref hits for %s"
;; remove carriage returns. They can make completion confusing.
(replace-regexp-in-string "\n" " " query)))
(candidates (let-alist json-data
(cl-loop for item across .message.items
collect (let-alist item
(cons (format "%s, %s, %s, %s."
(string-join .title " ")
(string-join
(cl-loop for author across .author collect
(let-alist author
(format "%s %s"
.given .family)))
", ")
.publisher
.created.date-parts)
.DOI)))))
(doi (cdr (assoc (completing-read "Choice: " candidates) candidates))))
(with-current-buffer (find-file-noselect bibtex-file)
(doi-utils-add-bibtex-entry-from-doi
(replace-regexp-in-string
"^https?://\\(dx.\\)?doi.org/" "" doi)
bibtex-file)
(save-buffer))))
(defalias 'crossref-add-bibtex-entry 'doi-utils-add-entry-from-crossref-query
"Alias function for convenience.")
;; * Convenience
(defun doi-utils-toggle-pdf-download ()
"Toggle the setting of `doi-utils-download-pdf'.
I find this useful when downloading the pdfs slows down adding a
lot of references; then you just toggle it off."
(interactive)
(message "Setting doi-utils-download-pdf to %s"
(setq doi-utils-download-pdf (not doi-utils-download-pdf))))
;;* The end
(provide 'doi-utils)
;;; doi-utils.el ends here
Reference in New Issue View Git Blame Copy Permalink