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.
+
+#+BEGIN_SRC emacs-lisp :notangle doi-utils.el
+(defmacro defpar (name &optional value)
+ `(progn (defvar ,name)
+ (setf ,name ,value)))
+
+(defpar 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))
+ (journal (plist-get results :container-title))
+ (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))
+ (month (elt (elt (plist-get (plist-get results :issued) :date-parts) 0) 1))
+ (pages (plist-get results :page))
+ (doi (plist-get results :DOI))
+ (url (plist-get results :URL))
+ (booktitle (plist-get results :container-title))))
+#+END_SRC
+
+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.
+
+#+BEGIN_SRC emacs-lisp :notangle doi-utils.el
+(defvar doi-utils-bibtex-type-generators nil)
+
+(defun concat-prepare (lst &optional acc)
+ "Given a list `lst' of strings and other expressions, which are
+intented to passed to `concat', concat any subsequent strings,
+minimising the number of arguments being passed to `concat'
+without changing the results."
+ (cond ((null lst) (nreverse acc))
+ ((and (stringp (car lst))
+ (stringp (car acc)))
+ (concat-prepare (cdr lst) (cons (concat (car acc) (car lst))
+ (cdr acc))))
+ (t (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' with
+`fields' (given as symbols), matching 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' - a list of strings."
+ `(push (lambda (type results)
+ (when (or ,@(mapcar (lambda (match-type) `(string= type ,match-type)) matching-types))
+ (let ,(mapcar (lambda (field) (or (assoc field doi-utils-json-metadata-extract)
+ (error "unknown bibtex field type %s" field)))
+ fields)
+ (concat
+ ,@(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)
+ `(,(concat " " (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)
+#+END_SRC
+
+With the code generating the bibtex entry in place, we can glue it to the json retrieval code.
+#+BEGIN_SRC emacs-lisp :notangle doi-utils.el
+(defun doi-utils-doi-to-bibtex-string (doi)
+ "return a bibtex entry as a string for the doi. Only articles are currently supported"
+ (let* ((results (doi-utils-get-json-metadata doi))
+ (type (plist-get results :type)))
+ (format "%s" results) ; json-data
+ (some (lambda (g) (funcall g type results)) doi-utils-bibtex-type-generators)
+ (message-box "%s not supported yet." type)))
+#+END_SRC
+
+
#+BEGIN_SRC emacs-lisp :tangle doi-utils.el
(defun doi-utils-doi-to-bibtex-string (doi)
"return a bibtex entry as a string for the doi. Only articles are currently supported"
(s-match "^10" (buffer-substring
(region-beginning)
(region-end))))
- (buffer-susbstring (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.
((if (s-match "^10" (car kill-ring))
* Adding a bibtex entry from a crossref query
+The idea here is to perform a query on Crossref, get a helm 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.
#+BEGIN_SRC emacs-lisp :tangle doi-utils.el
(defun doi-utils-add-entry-from-crossref-query (query bibtex-file)
(cond
;; If region is active assume we want it
((region-active-p)
- (buffer-susbstring (region-beginning) (region-end)))
+ (replace-regexp-in-string
+ "\n" " "
+ (buffer-substring (region-beginning) (region-end))))
;; type or paste it in
(t
nil)))
(setq json-string (buffer-substring url-http-end-of-headers (point-max)))
(setq json-data (json-read-from-string json-string)))
- (let* ((name (format "Crossref hits for %s" query))
+ (let* ((name (format "Crossref hits for %s"
+ ;; remove carriage returns. they cause problems in helm.
+ (replace-regexp-in-string "\n" " " query)))
(helm-candidates (mapcar (lambda (x)
(cons
(concat
;; just return the candidate
(action . (("Insert bibtex entry" . (lambda (doi)
(doi-utils-add-bibtex-entry-from-doi
- (replace-regexp-in-string "^http://dx.doi.org/" "" doi))))
+ (replace-regexp-in-string "^http://dx.doi.org/" "" doi) ,bibtex-file)))
("Open url" . (lambda (doi)
(browse-url doi))))))))
(helm :sources '(source)))))
#+END_EXAMPLE
-#+BEGIN_SRC emacs-lisp :var data=json :results value raw
+#+BEGIN_SRC emacs-lisp :var data=json :results value raw :tangle no
(let ((json-object-type 'plist)
(json (json-read-from-string data)))
(aref json 0))
Here is a list of helm candidates
-#+BEGIN_SRC emacs-lisp :var data=json :results code
+#+BEGIN_SRC emacs-lisp :var data=json :results code :tangle no
(let (;(json-object-type 'plist)
(json (json-read-from-string data)))
(mapcar (lambda (x) (cons (assoc 'fullCitation x) x)) json))
#+END_SRC
#+RESULTS:
-#+BEGIN_SRC emacs-lisp
+#+BEGIN_SRC emacs-lisp :tangle no
+
(((fullCitation . "Ann M. Deml, Vladan Stevanovi\304\207, Christopher L. Muhich, Charles B. Musgrave, Ryan O'Hayre, 2014, 'Oxide enthalpy of formation and band gap energy as accurate descriptors of oxygen vacancy formation energetics', <i>Energy & Environmental Science</i>, vol. 7, no. 6, p. 1996")
(year . "2014")
(coins . "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1039%2Fc3ee43874k&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Oxide+enthalpy+of+formation+and+band+gap+energy+as+accurate+descriptors+of+oxygen+vacancy+formation+energetics&rft.jtitle=Energy+%26+Environmental+Science&rft.date=2014&rft.volume=7&rft.issue=6&rft.spage=1996&rft.aufirst=Ann+M.&rft.aulast=Deml&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Ann+M.+Deml&rft.au=+Vladan+Stevanovi%C4%87&rft.au=+Christopher+L.+Muhich&rft.au=+Charles+B.+Musgrave&rft.au=+Ryan+O%27Hayre")
* ISBN utility
-This is not really a doi utility, but I am putting it here for now since it is just a single function. It looks up an ISBN and takes you to a page that has a bibtex entry. I am not crazy about that, but I have not found an isbn metadata source yet.
+These are not really doi utilities, but for now I am putting them here.
+
+I found this on the web. It can be handy, but the bibtex entry has a lot of stuff in it.
#+BEGIN_SRC emacs-lisp :tangle doi-utils.el
-(defun isbn-to-bibtex (isbn)
+(defun isbn-to-bibtex-lead (isbn)
"Search lead.to for ISBN bibtex entry. You have to copy the entry if it is on the page to your bibtex file."
- (interactive "ISBN: ")
+ (interactive "sISBN: ")
(browse-url
(format "http://lead.to/amazon/en/?key=%s+&si=all&op=bt&bn=&so=sa&ht=us" isbn)))
#+END_SRC
+
+Here we get isbn metadata and build a bibtex entry.
+http://xisbn.worldcat.org/xisbnadmin/doc/api.htm#getmetadata
+
+
+#+BEGIN_SRC emacs-lisp :tangle doi-utils.el
+(defun isbn-to-bibtex (isbn bibfile)
+ "Get bibtex entry for ISBN and insert it into BIBFILE unless an
+entry with the generated key already exists in the file."
+ (interactive
+ (list
+ (read-input
+ "ISBN: "
+ ;; now set initial input
+ (cond
+ ;; If region is active and it starts with a number, we use it
+ ((and (region-active-p)
+ (s-match "^[0-9]" (buffer-substring (region-beginning) (region-end))))
+ (buffer-substring (region-beginning) (region-end)))
+ ;; if first entry in kill ring starts with a number assume it is an isbn
+ ;; and use it as the guess
+ ((if (s-match "^[0-9]" (car kill-ring))
+ (car kill-ring)))
+ ;; type or paste it in
+ (t
+ nil)))
+ (ido-completing-read
+ "Bibfile: "
+ (append (f-entries "." (lambda (f) (f-ext? f "bib")))
+ org-ref-default-bibliography))))
+
+ (let* ((results (with-current-buffer
+ (url-retrieve-synchronously
+ (format
+ "http://xisbn.worldcat.org/webservices/xid/isbn/%s?method=getMetadata&format=json&fl=*"
+ isbn))
+ (json-read-from-string
+ (buffer-substring url-http-end-of-headers (point-max)))))
+ (status (cdr (nth 1 results)))
+ (metadata (aref (cdar results) 0))
+ (new-entry)
+ (new-key))
+
+ ;; check if we got something
+ (unless (string= "ok" status)
+ (error "Status is %s" status))
+
+ ;; construct an alphabetically sorted bibtex entry. I assume ISBN numbers go
+ ;; with book entries.
+ (setq new-entry
+ (concat "\n@book{,\n"
+ (mapconcat
+ 'identity
+ (loop for field in (-sort 'string-lessp (mapcar 'car metadata))
+ collect
+ (format " %s={%s}," field (cdr (assoc field metadata))))
+ "\n")
+ "\n}\n"))
+
+ ;; build entry in temp buffer to get the key so we can check for duplicates
+ (setq new-entry (with-temp-buffer
+ (insert new-entry)
+ (org-ref-clean-bibtex-entry)
+ (setq new-key (bibtex-key-in-head))
+ (buffer-string)))
+ (find-file bibfile)
+ (goto-char (point-min))
+ (when (search-forward new-key nil t)
+ (beep)
+ (setq new-key (read-input
+ (format "%s already exists. Enter new key (C-g to cancel): " new-key)
+ new-key)))
+ (goto-char (point-max))
+ (insert new-entry)
+ ;; set key. It is simplest to just replace it, even if it is the same.
+ (bibtex-beginning-of-entry)
+ (re-search-forward bibtex-entry-maybe-empty-head)
+ (if (match-beginning bibtex-key-in-head)
+ (delete-region (match-beginning bibtex-key-in-head)
+ (match-end bibtex-key-in-head)))
+ (insert new-key)
+ (bibtex-fill-entry)
+ (save-buffer)))
+#+END_SRC
+
+
+
* end of file
#+BEGIN_SRC emacs-lisp :tangle doi-utils.el
(provide 'doi-utils)
#+RESULTS:
: Loaded doi-utils.el
-
-
-
-
-
-#+BEGIN_SRC emacs-lisp
-(setq data '(("John" . "john@email.com")
- ("Jim" . "jim@email.com")
- ("Jane" . "jane@email.com")
- ("Jill" . "jill@email.com")))
-
-(setq some-helm-source
- `((name . "HELM at the Emacs")
- (candidates . ,(mapcar 'car data))
- (action . (lambda (candidate)
- (message-box "%s" (cdr (assoc candidate data)))))))
-
-(message-box "you chose %s" (helm :sources '(some-helm-source)))
-#+END_SRC
-
-#+RESULTS:
-: you chose jim@email.com
projects / org-ref.git / blobdiff