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doi-utils.el
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;;; doi-utils.el --- DOI utilities for making bibtex entries
;; Copyright (C) 2015 John Kitchin
;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
;; Keywords: convenience
;; Version: 0.1
;; 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-add-bibtex-entry-from-region to add an entry from a highlighed doi to your default bibliography.
;; - doi-utils-update-bibtex-entry-from-doi with cursor in an entry to update its fields.
(require 'bibtex)
(eval-when-compile
(require 'cl))
(require 'dash)
(require 'json)
(require 'org) ; org-add-link-type
(require 'org-bibtex) ; org-bibtex-yank
;;; Code:
;;* 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-make-file-field
nil
"Make a bibtex field for the downloaded PDF file."
: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 nil to avoid setting timestamps in the entries."
:type 'function
:group 'doi-utils)
(defcustom doi-utils-make-notes-function
(lambda ()
(bibtex-beginning-of-entry)
(helm-bibtex-edit-notes (cdr (assoc "=key=" (bibtex-parse-entry))) ))
"Function to create notes for a bibtex entry.
For all notes in the `org-ref-bibliography-notes' use
`org-ref-open-bibtex-notes' as the function.
Set to (lambda () nil) if you want no notes."
:type 'function
:group 'doi-utils)
;;* Getting pdf files from a DOI
;; The idea here is simple. When you visit http://dx.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 dx.DOI.org/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 "http://dx.doi.org/%s" 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://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://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://www.nature.com" *doi-utils-redirect*)
(let ((result *doi-utils-redirect*))
(setq result (replace-regexp-in-string "/full/" "/pdf/" result))
(replace-regexp-in-string "\.html$" "\.pdf" result))))
;;** 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
;; http://onlinelibrary.wiley.com/doi/10.1002/anie.201402680/abstract
;; http://onlinelibrary.wiley.com/doi/10.1002/anie.201402680/pdf
;; It appears that it is not enough to use the pdf url above. That takes you to
;; an html page. The actual link to teh pdf is embedded in that page. This is
;; how ScienceDirect does things too.
;; This is where the link is hidden:
;; <iframe id="pdfDocument" src="http://onlinelibrary.wiley.com/store/10.1002/anie.201402680/asset/6397_ftp.pdf?v=1&t=hwut2142&s=d4bb3cd4ad20eb733836717f42346ffb34017831" width="100%" height="675px"></iframe>
(defun doi-utils-get-wiley-pdf-url (redirect-url)
"Wileyscience direct hides the pdf url in html.
We get it out here by parsing the html.
Argument REDIRECT-URL URL you are redirected to."
(setq *doi-utils-waiting* t)
(url-retrieve
redirect-url
(lambda (status)
(goto-char (point-min))
(re-search-forward "<iframe id=\"pdfDocument\" src=\"\\([^\"]*\\)\"" nil)
(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 wiley-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http://onlinelibrary.wiley.com" *doi-utils-redirect*)
(doi-utils-get-wiley-pdf-url
(replace-regexp-in-string "/abstract" "/pdf" *doi-utils-redirect*))
*doi-utils-pdf-url*))
;;** Springer
(defun springer-chapter-pdf-url (*doi-utils-redirect*)
(when (string-match "^http://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://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://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://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://iopscience.iop.org" *doi-utils-redirect*)
(let ((tail (replace-regexp-in-string
"^http://iopscience.iop.org" "" *doi-utils-redirect*)))
(concat "http://iopscience.iop.org" tail
"/pdf" (replace-regexp-in-string "/" "_" tail) ".pdf"))))
;;** JSTOR
(defun jstor-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http://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://scitation.aip.org" *doi-utils-redirect*)
;; get stuff after content
(let (p1 p2 s p3)
(setq p2 (replace-regexp-in-string
"^http://scitation.aip.org/" "" *doi-utils-redirect*))
(setq s (split-string p2 "/"))
(setq p1 (mapconcat 'identity (-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))))
;;** Taylor and Francis
(defun tandfonline-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http://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://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://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://pubs.rsc.org" *doi-utils-redirect*)
(let ((url (downcase *doi-utils-redirect*)))
(setq url (replace-regexp-in-string "articlelanding" "articlepdf" url))
url)))
;;** Science Direct
(defun doi-utils-get-science-direct-pdf-url (redirect-url)
"Science direct hides the pdf url in html. W 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 "pdfurl=\"\\([^\"]*\\)\"" 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 science-direct-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http://www.sciencedirect.com" *doi-utils-redirect*)
(doi-utils-get-science-direct-pdf-url *doi-utils-redirect*)
*doi-utils-pdf-url*))
;; sometimes I get
;; http://linkinghub.elsevier.com/retrieve/pii/S0927025609004558
;; which actually redirect to
;; http://www.sciencedirect.com/science/article/pii/S0927025609004558
(defun linkinghub-elsevier-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match
"^http://linkinghub.elsevier.com/retrieve" *doi-utils-redirect*)
(let ((second-redirect (replace-regexp-in-string
"http://linkinghub.elsevier.com/retrieve"
"http://www.sciencedirect.com/science/article"
*doi-utils-redirect*)))
*doi-utils-pdf-url*)))
;;** 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://www.pnas.org" *doi-utils-redirect*)
(concat *doi-utils-redirect* ".full.pdf?with-ds=yes")))
;;** Sage
(defun sage-pdf-url (*doi-utils-redirect*)
"Get url to the pdf from *DOI-UTILS-REDIRECT*."
(when (string-match "^http://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://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://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6912247
;; http://ieeexplore.ieee.org/ielx7/6903646/6912234/06912247.pdf
;; http://ieeexplore.ieee.org/iel7/6903646/6912234/06912247.pdf?arnumber=6912247
;; <meta name="citation_pdf_url" content="http://ieeexplore.ieee.org/iel7/6903646/6912234/06912247.pdf?arnumber=6912247">
(defun ieee-pdf-url (*doi-utils-redirect*)
"Get a url to the pdf from *DOI-UTILS-REDIRECT* for IEEE urls."
(when (string-match "^http://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:]]*?\\)\">")
(match-string 1)))))
;;** Add all functions
(setq doi-utils-pdf-url-functions
(list
'aps-pdf-url
'science-pdf-url
'nature-pdf-url
'wiley-pdf-url
'springer-chapter-pdf-url
'springer-pdf-url
'acs-pdf-url-1
'acs-pdf-url-2
'iop-pdf-url
'jstor-pdf-url
'aip-pdf-url
'science-direct-pdf-url
'linkinghub-elsevier-pdf-url
'tandfonline-pdf-url
'ecs-pdf-url
'ecst-pdf-url
'rsc-pdf-url
'pnas-pdf-url
'sage-pdf-url
'jneurosci-pdf-url
'ieee-pdf-url
'generic-full-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
;;;###autoload
(defun doi-utils-get-bibtex-entry-pdf ()
"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
to `org-ref-pdf-directory', 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."
(interactive)
(save-excursion
(bibtex-beginning-of-entry)
(let (;; get doi, removing http://dx.doi.org/ if it is there.
(doi (replace-regexp-in-string
"http://dx.doi.org/" ""
(bibtex-autokey-get-field "doi")))
(key)
(pdf-url)
(pdf-file)
(content))
;; get the key and build pdf filename.
(re-search-forward bibtex-entry-maybe-empty-head)
(setq key (match-string bibtex-key-in-head))
(setq pdf-file (concat
(if org-ref-pdf-directory
(file-name-as-directory org-ref-pdf-directory)
(read-directory-name "PDF directory: " "."))
key ".pdf"))
;; now get file if needed.
(when (and doi (not (file-exists-p pdf-file)))
(setq pdf-url (doi-utils-get-pdf-url doi))
(if pdf-url
(progn
(url-copy-file pdf-url pdf-file)
;; now check if we got a pdf
(with-temp-buffer
(insert-file-contents pdf-file)
;; PDFS start with %PDF-1.x as the first few characters.
(if (not (string= (buffer-substring 1 (min 6 (point-max))) "%PDF-"))
(progn
(delete-file pdf-file)
(message "No pdf was downloaded.")
(browse-url pdf-url))
(message "%s saved" pdf-file)))
;; make a bibtex field for the file if necessary
(when doi-utils-make-file-field
(bibtex-make-field `("file" ""
,(concat key ".pdf:"
key ".pdf:PDF")) t))
(when (and doi-utils-open-pdf-after-download (file-exists-p pdf-file))
(org-open-file pdf-file))))
pdf-file))))
;;* Getting bibtex entries from a DOI
;; I
;; [[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.
;; This is a local variable defined in `url-http'. We need it to avoid
;; byte-compiler errors.
(defvar-local url-http-end-of-headers nil)
(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."
(let ((url-request-method "GET")
(url-mime-accept-string "application/citeproc+json")
(json-object-type 'plist)
(json-data))
(with-current-buffer
(url-retrieve-synchronously
(concat "http://dx.doi.org/" doi))
(setq json-data (buffer-substring url-http-end-of-headers (point-max)))
(if (string-match "Resource not found" json-data)
(progn
(browse-url (concat "http://dx.doi.org/" doi))
(error "Resource not found. Opening website"))
(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) (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 (elt (elt (plist-get (plist-get results :issued) :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))))
;; 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
(-flatten
(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")
author title journal year volume number pages doi url)
(doi-utils-def-bibtex-type inproceedings ("proceedings-article")
author title booktitle year month pages doi url)
(doi-utils-def-bibtex-type book ("book")
author title series publisher year pages doi url)
(doi-utils-def-bibtex-type inbook ("book-chapter")
author title booktitle series publisher year pages 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 (doi-utils-get-json-metadata doi))
(type (plist-get results :type)))
;; (format "%s" results) ; json-data
(or (-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, and create a notes entry for
;; you.
(defun doi-utils-insert-bibtex-entry-from-doi (doi)
"Insert bibtex entry from a DOI.
Also cleans entry using ‘org-ref’, and tries to download the corresponding pdf."
(insert (doi-utils-doi-to-bibtex-string doi))
(backward-char)
;; set date added for the record
(when doi-utils-timestamp-format-function
(bibtex-set-field doi-utils-timestamp-field
(funcall doi-utils-timestamp-format-function)))
(org-ref-clean-bibtex-entry)
;; try to get pdf
(when doi-utils-download-pdf
(doi-utils-get-bibtex-entry-pdf))
(save-selected-window
(org-ref-open-bibtex-notes)
;;(save-buffer) ; helm-bibtex-edit-notes performs a search in the buffer that fails if the buffer has not been saved
;;(funcall doi-utils-make-notes-function)
))
;; It may be you are in some other place when you want to add a bibtex entry.
;; This next function will open the first entry in org-ref-default-bibliography
;; go to the end, and add the entry. You can sort it later.
;;;###autoload
(defun doi-utils-add-bibtex-entry-from-doi (doi bibfile)
"Add DOI entry to end of a file in the current directory.
Pick the file ending with .bib or in
`org-ref-default-bibliography'. 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 intial 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
(cond
;; If region is active and it starts like a doi we want it.
((and (region-active-p)
(s-match "^10" (buffer-substring
(region-beginning)
(region-end))))
(buffer-substring (region-beginning) (region-end)))
;; if the first entry in the kill-ring looks
;; like a DOI, let's use it.
((and
;; make sure the kill-ring has something in it
(stringp (car kill-ring))
(s-match "^10" (car kill-ring)))
(car kill-ring))
;; otherwise, we have no initial input. You
;; will have to type it in.
(t
nil)))
;; now get the bibfile to add it to
(ido-completing-read
"Bibfile: "
(append (f-entries "." (lambda (f)
(and (not (string-match "#" f))
(f-ext? f "bib"))))
org-ref-default-bibliography))))
;; 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 (search-forward doi nil t)
(message "%s is already in this file" doi)
(goto-char (point-max))
(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.")
;;;###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))))
;; The updating function for a whole entry looks like this. We get all the keys
;; from the json plist metadata, and update the fields if they exist.
(defun plist-get-keys (plist)
"Return keys in a PLIST."
(-slice plist 0 nil 2))
;;;###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
"http://dx.doi.org/" ""
(bibtex-autokey-get-field "doi"))
(read-string "DOI: "))))
(let* ((results (doi-utils-get-json-metadata doi))
(type (plist-get results :type))
(author (mapconcat
(lambda (x) (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 (doi-utils-get-json-metadata 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")))
;;* 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 "http://dx.doi.org/" doi)))
;;;###autoload
(defun doi-utils-open-bibtex (doi)
"Search through variable `reftex-default-bibliography' for DOI."
(interactive "sDOI: ")
(catch 'file
(dolist (f reftex-default-bibliography)
(find-file f)
(when (search-forward doi (point-max) t)
(bibtex-beginning-of-entry)
(throw 'file t)))))
;;;###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))))
(defvar doi-link-menu-funcs '()
"Functions to run in doi menu.
Each entry is a list of (key menu-name function). The function
must take one argument, the doi.")
(setq doi-link-menu-funcs
'(("o" "pen" doi-utils-open)
("w" "os" doi-utils-wos)
("c" "iting articles" doi-utils-wos-citing)
("r" "elated articles" doi-utils-wos-related)
("s" "Google Scholar" doi-utils-google-scholar)
("f" "CrossRef" doi-utils-crossref)
("p" "ubmed" doi-utils-pubmed)