#+END_SRC
* 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.
+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.
+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.
#+BEGIN_SRC emacs-lisp :tangle doi-utils.el
(defvar *doi-utils-waiting* t
;; 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
+ (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
(replace-regexp-in-string "/abs/" "/pdf/" *doi-utils-redirect*)))
#+END_SRC
-#+BEGIN_SRC emacs-lisp
+#+BEGIN_SRC emacs-lisp :tangle no
(acs-pdf-url "http://pubs.acs.org/doi/abs/10.1021/nl500037x")
#+END_SRC
(concat (replace-regexp-in-string "/stable/" "/stable/pdfplus/" *doi-utils-redirect*) ".pdf")))
#+END_SRC
-** AIP
+** AIP
#+BEGIN_SRC emacs-lisp :tangle doi-utils.el
(defun aip-pdf-url (*doi-utils-redirect*)
(when (string-match "^http://scitation.aip.org" *doi-utils-redirect*)
'aps-pdf-url
'science-pdf-url
'nature-pdf-url
- 'wiley-pdf-url
+ 'wiley-pdf-url
'springer-pdf-url
'acs-pdf-url
'iop-pdf-url
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))
(message "applying functions")
at the end."
(interactive)
(save-excursion
- (bibtex-beginning-of-entry)
+ (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")))
+ (bibtex-autokey-get-field "doi")))
(key)
(pdf-url)
(pdf-file)
(message "%s" (buffer-string))
(delete-file pdf-file))
(message "%s saved" pdf-file)))
-
+
(when (file-exists-p pdf-file)
(org-open-file pdf-file)))
(message "No pdf-url found for %s at %s" doi *doi-utils-redirect* ))
#+BEGIN_SRC emacs-lisp :tangle doi-utils.el
(defun doi-utils-get-json-metadata (doi)
-
- (let ((url-request-method "GET")
+ "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))
(url-retrieve-synchronously
(concat "http://dx.doi.org/" doi))
(setq json-data (buffer-substring url-http-end-of-headers (point-max)))
- (message "%s" json-data)
- (json-read-from-string json-data))))
+ (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)))))
#+END_SRC
#+RESULTS:
(cond
((or (string= type "journal-article") (string= type "article-journal"))
(doi-utils-expand-template "@article{,
- author = {%{author}},
- title = {%{title}},
- journal = {%{journal}},
- year = {%{year}},
- volume = {%{volume}},
- number = {%{issue}},
- pages = {%{pages}},
+ author = {%{author}},
+ title = {%{title}},
+ journal = {%{journal}},
+ year = {%{year}},
+ volume = {%{volume}},
+ number = {%{issue}},
+ pages = {%{pages}},
doi = {%{doi}},
url = {%{url}},
}"))
-
+
((string= type "proceedings-article")
(setq booktitle (plist-get results :container-title))
(doi-utils-expand-template "@inproceedings{,
- author = {%{author}},
- title = {%{title}},
+ author = {%{author}},
+ title = {%{title}},
booktitle = {%{booktitle}},
- year = {%{year}},
- month = {%{month}},
- pages = {%{pages}},
+ year = {%{year}},
+ month = {%{month}},
+ pages = {%{pages}},
doi = {%{doi}},
url = {%{url}},
}"))
-
+
(t (message-box "%s not supported yet." type)))))
#+END_SRC
#+RESULTS:
#+begin_example
@article{,
- author = {F. Abild-Pedersen and J. Greeley and F. Studt and J. Rossmeisl and T. Munter and P. Moses and E. Skúlason and T. Bligaard and J. Nørskov},
- title = {Scaling Properties of Adsorption Energies for Hydrogen-Containing Molecules on Transition-Metal Surfaces},
- journal = {Phys. Rev. Lett.},
- year = {2007},
- volume = {99},
- number = {1},
- pages = {nil},
+ author = {F. Abild-Pedersen and J. Greeley and F. Studt and J. Rossmeisl and T. Munter and P. Moses and E. Skúlason and T. Bligaard and J. Nørskov},
+ title = {Scaling Properties of Adsorption Energies for Hydrogen-Containing Molecules on Transition-Metal Surfaces},
+ journal = {Phys. Rev. Lett.},
+ year = {2007},
+ volume = {99},
+ number = {1},
+ pages = {nil},
doi = {10.1103/physrevlett.99.016105},
url = {http://dx.doi.org/10.1103/PhysRevLett.99.016105},
}
(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."
- (interactive "sDOI: ")
+ (interactive "sDOI :")
(insert (doi-utils-doi-to-bibtex-string doi))
(backward-char)
(if (bibtex-key-in-head nil)
#+BEGIN_SRC emacs-lisp :tangle doi-utils.el
(defun doi-utils-add-bibtex-entry-from-doi (doi bibfile)
- "add entry to end a file in `org-ref-default-bibliography'."
+ "Add entry to end of a file in in the current directory 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 pste in a DOI."
(interactive
- (list
- (read-string "DOI: ")
- (ido-completing-read "Bibfile: " org-ref-default-bibliography)))
- (find-file bibfile)
- (goto-char (point-min))
- (if (search-forward doi nil t)
- (message "%s is already in this file" doi)
- (end-of-buffer)
- (insert "\n\n")
- (doi-utils-insert-bibtex-entry-from-doi doi)
- (save-buffer)))
+ (list (read-input "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-susbstring (region-beginning) (region-end)))
+ ;; if the first entry in the kill-ring looks
+ ;; like a DOI, let's use it.
+ ((if (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) (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
+ (find-file 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)
+ (end-of-buffer)
+ (insert "\n\n")
+ (doi-utils-insert-bibtex-entry-from-doi doi)
+ (save-buffer))))
#+END_SRC
-It may be you want to just highlight a doi, and then add it. Here is that function.
-
-#+BEGIN_SRC emacs-lisp :tangle doi-utils.el
-(defun doi-utils-add-bibtex-entry-from-region (start end)
- "add entry assuming region is a doi to end of first entry in `org-ref-default-bibliography'."
- (interactive "r")
- (let ((doi (buffer-substring start end)))
- (find-file (car org-ref-default-bibliography))
- (end-of-buffer)
- (insert "\n")
- (doi-utils-insert-bibtex-entry-from-doi doi)))
-#+END_SRC
-
-#+RESULTS:
-: doi-utils-add-bibtex-entry-from-region
* 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.
(elt
(elt
(plist-get
- (plist-get results :issued) :date-parts) 0) 0)))
+ (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)))
-
+
;; 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))
(lambda (key)
(eval (cdr (assoc key mapping))))
(plist-get-keys results)))
-
+
; reclean entry, but keep key if it exists.
(if (bibtex-key-in-head)
(org-ref-clean-bibtex-entry t)
(defvar doi-link-menu-funcs '()
- "Functions to run in doi menu. Each entry is a list of (key menu-name function).
+ "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
(defun doi-link-menu (link-string)
- "Generate the link menu message, get choice and execute it.
+ "Generate the link menu message, get choice and execute it.
Options are stored in `doi-link-menu-funcs'."
(interactive)
(message
(char-to-string input) doi-link-menu-funcs)))
(when choice
(funcall
- (elt
+ (elt
choice
2)
link-string))))
'doi-link-menu)
#+END_SRC
-doi:10.1021/jp047349j
+doi:10.1021/jp047349j
* end of file
#+BEGIN_SRC emacs-lisp :tangle doi-utils.el
#+RESULTS:
: Loaded doi-utils.el
-
projects / org-ref.git / blobdiff