From 38e0713734282b6b4e1bc982bcf0f79cd9e3edaa Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Sun, 15 Mar 2015 22:17:17 -0400
Subject: [PATCH 01/16] ignore a few tex files.

---
 .gitignore | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.gitignore b/.gitignore
index 72f56ac..deab7c4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,3 +11,7 @@
 /org-ref.blg
 /org-ref.pdf
 /org-ref.tex
+/org-ref.ilg
+/org-ref.ind
+/org-ref.lof
+/org-ref.lot
-- 
2.39.2


From 3061355eb0479a302b7870223533aca5f2dc3f45 Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Sun, 15 Mar 2015 22:17:32 -0400
Subject: [PATCH 02/16] small space change.

---
 org-ref.el | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/org-ref.el b/org-ref.el
index cc3ac5f..ac6422a 100644
--- a/org-ref.el
+++ b/org-ref.el
@@ -504,7 +504,8 @@ Format according to the type in `org-ref-bibliography-entry-format'."
 		 (loop for file in org-ref-bibliography-files do
 		       (if (org-ref-key-in-file-p key (file-truename file))
 			   (throw 'result file)
-			 (message "%s not found in %s" key (file-truename file))))))
+			 (message "%s not found in %s"
+				  key (file-truename file))))))
 
     (with-temp-buffer
       (insert-file-contents file)
-- 
2.39.2


From 7a3f814ee1910b8e72b03224acf60b8df6a93dff Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Mon, 16 Mar 2015 08:38:11 -0400
Subject: [PATCH 03/16] add doc about new doi link.

---
 org-ref.org | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/org-ref.org b/org-ref.org
index 04e74b5..7a2ec5c 100644
--- a/org-ref.org
+++ b/org-ref.org
@@ -212,6 +212,8 @@ This will prompt you for a DOI, and a bibtex file, and then try to get the bibte
 - doi-utils-add-entry-from-crossref-query
 This will prompt you for a query string, which is usually the title of an article, or a free-form text citation of an article. Then you will get a helm buffer of matching items, which you can choose from to insert a new bibtex entry into a bibtex file.
 
+This library also redefines the org-mode doi link. Now, when you click on this link you will get a menu of options, e.g. to open a bibtex entry or a pdf if you have it, or to search the doi in some scientific search engines. Try it out  doi:10.1021/jp511426q.
+
 ** jmax-bibtex
 These are functions I use often in bibtex files.
 
-- 
2.39.2


From e620af30a93e5424e5c080c8eedeb85ac2af1567 Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Mon, 16 Mar 2015 08:42:23 -0400
Subject: [PATCH 04/16] Initial commit of wos.el

---
 wos.el | 63 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 wos.el

diff --git a/wos.el b/wos.el
new file mode 100644
index 0000000..e0a321a
--- /dev/null
+++ b/wos.el
@@ -0,0 +1,63 @@
+;;; wos.el --- WEb of Science functions              -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2015  John Kitchin
+
+;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
+;; Keywords:
+
+;; 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:
+
+;; Adds a new org-mode link for a search in Web of Science.
+
+
+;;; Code:
+(org-add-link-type
+ "wos"
+ (lambda (path)
+   (browse-url
+    (format  "http://gateway.webofknowledge.com/gateway/Gateway.cgi?topic=%s&GWVersion=2&SrcApp=WEB&SrcAuth=HSB&DestApp=UA&DestLinkType=GeneralSearchSummary"
+             (s-join "+"
+              (split-string path)))))
+ ;; formatting function. Assume html
+ (lambda (link desc format)
+   (format "<a href=\"%s\">%s</a>"
+           (format  "http://gateway.webofknowledge.com/gateway/Gateway.cgi?topic=%s&GWVersion=2&SrcApp=WEB&SrcAuth=HSB&DestApp=UA&DestLinkType=GeneralSearchSummary"
+             (s-join "+"
+              (split-string path)))
+           (format "wos:%s" link)
+           )))
+
+
+(defun wos-search ()
+  "Open the word at point or selection in Web of Science."
+  ;; the url was derived from this page: http://wokinfo.com/webtools/searchbox/
+  (interactive)
+  (browse-url
+   (format "http://gateway.webofknowledge.com/gateway/Gateway.cgi?topic=%s&GWVersion=2&SrcApp=WEB&SrcAuth=HSB&DestApp=UA&DestLinkType=GeneralSearchSummary"
+    (if (region-active-p)
+	(mapconcat 'identity (split-string
+			      (buffer-substring (region-beginning)
+						(region-end))) "+")
+      (thing-at-point 'word)))))
+
+
+(defun wos ()
+  "Open Web of Science search page in a browser."
+  (interactive)
+  (browse-url "http://apps.webofknowledge.com"))
+
+(provide 'wos)
+;;; wos.el ends here
-- 
2.39.2


From bc1db3fdfe710054d81dcb7b988aa683d872721f Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Mon, 16 Mar 2015 08:47:38 -0400
Subject: [PATCH 05/16] rename wos link to wos-search

---
 wos.el | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wos.el b/wos.el
index e0a321a..ff72a67 100644
--- a/wos.el
+++ b/wos.el
@@ -25,7 +25,7 @@
 
 ;;; Code:
 (org-add-link-type
- "wos"
+ "wos-search"
  (lambda (path)
    (browse-url
     (format  "http://gateway.webofknowledge.com/gateway/Gateway.cgi?topic=%s&GWVersion=2&SrcApp=WEB&SrcAuth=HSB&DestApp=UA&DestLinkType=GeneralSearchSummary"
-- 
2.39.2


From 10b2d2d87e4ec05edd0768069e88bcecce096584 Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Mon, 16 Mar 2015 08:48:19 -0400
Subject: [PATCH 06/16] add wos documentation

---
 org-ref.org | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/org-ref.org b/org-ref.org
index 7a2ec5c..297be57 100644
--- a/org-ref.org
+++ b/org-ref.org
@@ -283,6 +283,18 @@ Or this if you like key-chord:
 (key-chord-define-global "jj" 'jmax-bibtex-hydra/body)
 #+END_SRC
 
+** wos
+This is a small utility for Web of Science/Knowledge (http://apps.webofknowledge.com).
+
+#+BEGIN_SRC emacs-lisp
+(require 'wos)
+#+END_SRC
+
+- wos :: Convenience function to open WOK in a browser.
+- wos-search :: Search WOK with the selected text or word at point
+
+There is also a new org-mode link that opens a search: [[wos-search:alloy and segregation]]
+
 ** isbn
 index:isbn
 
-- 
2.39.2


From 061265b34f4f68f95a7c8ade91c1a558796c464b Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Mon, 16 Mar 2015 08:48:31 -0400
Subject: [PATCH 07/16] update contents

---
 README.org | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/README.org b/README.org
index b2622eb..3f3489b 100644
--- a/README.org
+++ b/README.org
@@ -9,19 +9,6 @@ See http://www.youtube.com/watch?v=Zya8SfmCtFA and https://www.youtube.com/watch
 
 [[./org-ref.org]] contains all documentation and installation instructions.
 
-[[./doi-utils.org]] contains functions for downloading bibtex entries from  a DOI, and redefines the org-mode doi link so it has more functionality.
-
-[[./jmax-bibtex.el]] contains some utility functions:
-
-1. jmax-bibtex runs a menu command with actions to run on a bibtex entry including looking up the doi for the entry in a variety of places, e.g. web of science related/citing articles, Google Scholar, Pubmed, and crossref, or opening a PDF associated with the entry.
-
-2. Bind M-n/M-p to next/previous bibtex entry.
-
-3. Sentence/title casing the title of a bibtex entry
-
-4. Function to replace non-ascii characters in bibtex entries
-
-5. Functions to replace journal names with @string entries, and corresponding short/long names.
 
 * Installation
 We are slowly moving towards getting org-ref in MELPA. Until then, here are some directions that will probably help install org-ref.
-- 
2.39.2


From 16eda27ba08102b87ab38dd0f52b0b09976beae7 Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Mon, 16 Mar 2015 16:27:37 -0400
Subject: [PATCH 08/16] add new function to find bad file links, bad
 \attachfile{} and attachfile links

for the org-ref command.
---
 org-ref.el | 37 +++++++++++++++++++++++++++++++++----
 1 file changed, 33 insertions(+), 4 deletions(-)

diff --git a/org-ref.el b/org-ref.el
index ac6422a..4509d2d 100644
--- a/org-ref.el
+++ b/org-ref.el
@@ -2395,7 +2395,7 @@ Makes a new buffer with clickable links."
           (kill-buffer "*Missing citations*"))
       (message "No bad cite links found"))))
 
-;; ** helm interface to bad citations, labels, refs in orgfile
+;; ** helm interface to bad citations, labels, refs and files in orgfile
 (defun org-ref-bad-cite-candidates ()
   "Return a list of conses (key . marker) where key does not exist in the known bibliography files, and marker points to the key."
   (let* ((cp (point))			; save to return to later
@@ -2482,6 +2482,29 @@ Makes a new buffer with clickable links."
 	    (goto-char cp)))))
       multiple-labels))
 
+(defun org-ref-bad-file-link-candidates ()
+  "Return list of conses (link . marker) wehre the file in the link does not exist."
+  (let* ((bad-files '()))
+    (org-element-map (org-element-parse-buffer) 'link
+      (lambda (link)
+	(let ((type (org-element-property :type link)))
+	  (when (or  (string= "file" type)
+		     (string= "attachfile" type))
+	    (unless (file-exists-p (org-element-property :path link))
+	      (add-to-list 'bad-files
+			   (cons (org-element-property :path link)
+				 (save-excursion
+				   (goto-char
+				    (org-element-property :begin link))
+				   (point-marker)))))))))
+    ;; Let us also check \attachfile{fname}
+    (save-excursion
+      (goto-char (point-min))
+      (while (re-search-forward "\\attachfile{\\(.*\\)}" nil t)
+	(unless (file-exists-p (match-string 1))
+	  (add-to-list 'bad-files (cons (match-string 1) (point-marker))))))
+    bad-files))
+
 ;;;###autoload
 (defun org-ref ()
   "Opens a helm interface to actions for org-ref.
@@ -2490,7 +2513,8 @@ Shows bad citations, ref links and labels"
   (let ((cb (current-buffer))
 	(bad-citations (org-ref-bad-cite-candidates))
 	(bad-refs (org-ref-bad-ref-candidates))
-	(bad-labels (org-ref-bad-label-candidates)))
+	(bad-labels (org-ref-bad-label-candidates))
+	(bad-files (org-ref-bad-file-link-candidates)))
 
     (helm :sources `(((name . "Bad citations")
 		       (candidates . ,bad-citations)
@@ -2510,6 +2534,12 @@ Shows bad citations, ref links and labels"
 					  (switch-to-buffer (marker-buffer marker))
 					  (goto-char marker))))
 		     ;;
+		     ((name . "Bad file links")
+		      (candidates . ,bad-files)
+		      (lambda (marker)
+				   (switch-to-buffer (marker-buffer marker))
+				   (goto-char marker)))
+		     ;;
 		     ((name . "Utilities")
 		      (candidates . (("Check buffer again" . org-ref)
 				     ("Insert citation" . helm-bibtex)
@@ -2534,8 +2564,7 @@ Shows bad citations, ref links and labels"
 				     ))
 		      (action . (lambda (x)
 				  (switch-to-buffer ,cb)
-				  (funcall x))))
-		      ))))
+				  (funcall x))))))))
 
 ;; ** Find non-ascii charaters
 (defun org-ref-find-non-ascii-characters ()
-- 
2.39.2


From d25e6dc1a7148a4d8d35c97e5032f68fb3922a01 Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Tue, 17 Mar 2015 15:47:02 -0400
Subject: [PATCH 09/16] adjusted cite link re to fix issue #23

https://github.com/jkitchin/org-ref/issues/23
---
 org-ref.el | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/org-ref.el b/org-ref.el
index ac6422a..fefd831 100644
--- a/org-ref.el
+++ b/org-ref.el
@@ -326,7 +326,7 @@ You will see a message in the minibuffer when on a cite, ref or label link."
 		       (replace-regexp-in-string "\*" "\\\\*" x)
 		       )
 		     org-ref-cite-types "\\|") "\\)"
-  ":\\([a-zA-Z0-9-_:]*,?\\)*"))
+  ":\\([a-zA-Z0-9-_:\\.]*,?\\)*"))
 
 
 (setq org-ref-label-re
-- 
2.39.2


From 91014fe9da3996754cf62ffc6177f8813eb38bad Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Tue, 17 Mar 2015 18:45:00 -0400
Subject: [PATCH 10/16] shortened description

got rid of lexical variable at the top. I don't think I need it, it was inserted by auto-insert. moved Package-requires up with rest of package info.
---
 doi-utils.el | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doi-utils.el b/doi-utils.el
index 74c0045..abfa943 100644
--- a/doi-utils.el
+++ b/doi-utils.el
@@ -1,9 +1,11 @@
-;;; doi-utils.el --- DOI utilities for making bibtex entries and downloading PDFs  -*- lexical-binding: t; -*-
+;;; 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
@@ -30,8 +32,6 @@
 ;; - 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.
 
-;; Package-Requires: ((org-ref))
-
 (require 'json)
 
 ;;; Code:
-- 
2.39.2


From ca0d4bbfa864ceb371eef35f36987f8f9a7b7679 Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Tue, 17 Mar 2015 18:48:05 -0400
Subject: [PATCH 11/16] fix typo in wiley-pdf

left over comma from org-block escaping an *.
---
 doi-utils.el | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/doi-utils.el b/doi-utils.el
index abfa943..385785a 100644
--- a/doi-utils.el
+++ b/doi-utils.el
@@ -116,14 +116,15 @@
 
 
 (defun doi-utils-get-wiley-pdf-url (redirect-url)
-  "wileyscience direct hides the pdf url in html. we get it out here"
+  "Wileyscience direct hides the pdf url in html.
+We get it out here by parsing the html."
   (setq *doi-utils-waiting* t)
   (url-retrieve redirect-url
 		(lambda (status)
-		  (beginning-of-buffer)
+		  (goto-char (point-min))
 		  (re-search-forward "<iframe id=\"pdfDocument\" src=\"\\([^\"]*\\)\"" nil)
 		  (setq *doi-utils-pdf-url* (match-string 1)
-			,*doi-utils-waiting* nil)))
+			*doi-utils-waiting* nil)))
   (while *doi-utils-waiting* (sleep-for 0.1))
   *doi-utils-pdf-url*)
 
-- 
2.39.2


From 03f43f5e1f5f7ea61b19e0f0b428d7caa2e9ee5f Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Tue, 17 Mar 2015 18:48:55 -0400
Subject: [PATCH 12/16] fix two other ,* typos

---
 doi-utils.el | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doi-utils.el b/doi-utils.el
index 385785a..9d65393 100644
--- a/doi-utils.el
+++ b/doi-utils.el
@@ -227,7 +227,7 @@ We get it out here by parsing the html."
 		  (beginning-of-buffer)
 		  (re-search-forward "pdfurl=\"\\([^\"]*\\)\"" nil t)
 		  (setq *doi-utils-pdf-url* (match-string 1)
-			,*doi-utils-waiting* nil)))
+			*doi-utils-waiting* nil)))
   (while *doi-utils-waiting* (sleep-for 0.1))
   *doi-utils-pdf-url*)
 
@@ -246,7 +246,7 @@ We get it out here by parsing the html."
     (let ((second-redirect (replace-regexp-in-string
 			    "http://linkinghub.elsevier.com/retrieve"
 			    "http://www.sciencedirect.com/science/article"
-			    ,*doi-utils-redirect*)))
+			    *doi-utils-redirect*)))
       (message "getting pdf url from %s" second-redirect)
       *doi-utils-pdf-url*)))
 
-- 
2.39.2


From eae7aadab5856b4c65a6bd72a1914f5d6b0c6dc7 Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Tue, 17 Mar 2015 18:55:05 -0400
Subject: [PATCH 13/16] a round of checkdoc fixing

---
 doi-utils.el | 59 +++++++++++++++++++++++++++-------------------------
 1 file changed, 31 insertions(+), 28 deletions(-)

diff --git a/doi-utils.el b/doi-utils.el
index 9d65393..4e80d16 100644
--- a/doi-utils.el
+++ b/doi-utils.el
@@ -22,7 +22,7 @@
 
 ;;; 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.
+;; 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:
 
@@ -41,13 +41,13 @@
 ;; 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.")
+  "Stores waiting state for url retrieval.")
 
 (defvar *doi-utils-redirect* nil
-  "stores redirect url from a callback function")
+  "Stores redirect url from a callback function.")
 
 (defun doi-utils-redirect-callback (&optional status)
-  "callback for url-retrieve to set the redirect"
+  "Callback for url-retrieve to set the redirect."
   (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
@@ -60,7 +60,7 @@
 ;; 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"
+  "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.
@@ -78,7 +78,7 @@
 ;; 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
-  "list of 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.")
+  "List of 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
@@ -220,7 +220,7 @@ We get it out here by parsing the html."
   "stores url to pdf download from a callback function")
 
 (defun doi-utils-get-science-direct-pdf-url (redirect-url)
-  "science direct hides the pdf url in html. we get it out here"
+  "Science direct hides the pdf url in html. we get it out here."
   (setq *doi-utils-waiting* t)
   (url-retrieve redirect-url
 		(lambda (status)
@@ -286,8 +286,8 @@ We get it out here by parsing the html."
 ;; ** Get the pdf url for a doi
 
 (defun doi-utils-get-pdf-url (doi)
-  "returns a url to a pdf for the doi if one can be
-calculated. Loops through the functions in `doi-utils-pdf-url-functions'
+  "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)
 
@@ -306,12 +306,12 @@ until one is found"
 ;; ** Finally, download the pdf
 
 (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
+  "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
+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
+page.  you must have permission to access the pdf.  We open the pdf
 at the end."
   (interactive)
   (save-excursion
@@ -355,7 +355,7 @@ at the end."
 ;; 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.
 
 (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."
+  "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)
@@ -367,14 +367,14 @@ at the end."
       (if (string-match "Resource not found" json-data)
 	  (progn
 	    (browse-url (concat "http://dx.doi.org/" doi))
-	    (error "Resource not found. Opening website."))
+	    (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 template containing %{} with the eval of its contents"
+  "Expand a template containing %{} with the eval of its contents."
   (replace-regexp-in-string "%{\\([^}]+\\)}"
                             (lambda (arg)
                               (let ((sexp (substring arg 2 -1)))
@@ -434,7 +434,7 @@ when the `:type' parameter in the JSON metadata is contained in
                                (if field-expr
                                    ;; need to convert to string first
                                    `(,(car field-expr) (format "%s" ,(cadr field-expr)))
-                                   (error "unknown bibtex field type %s" field))))
+                                   (error "Unknown bibtex field type %s" field))))
                            fields)
                (concat
                 ,@(doi-utils-concat-prepare
@@ -465,7 +465,7 @@ when the `:type' parameter in the JSON metadata is contained in
 ;; 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."
+  "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
@@ -476,8 +476,8 @@ when the `:type' parameter in the JSON metadata is contained in
 
 
 (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 bibtex entry from a DOI.
+Also cleans entry using org-ref, and tries to download the corresponding pdf."
   (interactive "sDOI :")
   (insert (doi-utils-doi-to-bibtex-string doi))
   (backward-char)
@@ -546,7 +546,7 @@ prompt. Otherwise, you have to type or pste in a DOI."
 
 
 (defun bibtex-set-field (field value &optional nodelim)
-  "set field to value in bibtex file. create field if it does not exist"
+  "Set FIELD to VALUE in bibtex file. create field if it does not exist."
   (interactive "sfield: \nsvalue: ")
   (bibtex-beginning-of-entry)
   (let ((found))
@@ -574,12 +574,12 @@ prompt. Otherwise, you have to type or pste in a DOI."
 
 
 (defun plist-get-keys (plist)
-   "return keys in a plist"
+   "Return keys in a PLIST."
   (loop
    for key in results by #'cddr collect key))
 
 (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 changes will be lost."
+  "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: "))))
@@ -629,6 +629,8 @@ prompt. Otherwise, you have to type or pste in a DOI."
 
 
 (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))
@@ -658,14 +660,14 @@ prompt. Otherwise, you have to type or pste in a DOI."
 ;; 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.
 
 (defun doi-utils-wos (doi)
-  "Open Web of Science entry for 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)))
 
 (defun doi-utils-wos-citing (doi)
-  "Open Web of Science citing articles entry. May be empty if none are found"
+  "Open Web of Science citing articles entry. May be empty if none are found."
   (interactive "sDOI: ")
   (browse-url
    (concat
@@ -700,7 +702,7 @@ prompt. Otherwise, you have to type or pste in a DOI."
 
 
 (defun doi-utils-open-bibtex (doi)
-  "Search through `reftex-default-bibliography' for DOI."
+  "Search through variable `reftex-default-bibliography' for DOI."
   (interactive "sDOI: ")
   (catch 'file
     (dolist (f reftex-default-bibliography)
@@ -719,7 +721,7 @@ prompt. Otherwise, you have to type or pste in a DOI."
 
 
 (defun doi-utils-google-scholar (doi)
-  "Google scholar the word at point or selection."
+  "Google scholar the DOI."
   (interactive "sDOI: ")
   (browse-url
    (format
@@ -727,7 +729,7 @@ prompt. Otherwise, you have to type or pste in a DOI."
 
 
 (defun doi-utils-pubmed (doi)
-  "Pubmed the word at point or selection."
+  "Search Pubmed for the DOI."
   (interactive "sDOI: ")
   (browse-url
    (format
@@ -881,6 +883,7 @@ error."
 ;; 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.
 
 (defun doi-utils-add-entry-from-crossref-query (query bibtex-file)
+  "Search Crossref with QUERY and use helm to select an entry to add to BIBTEX-FILE."
   (interactive (list
 		(read-input
 		 "Query: "
-- 
2.39.2


From a28522b48c126dba09e182ae3a790bc2f94f56ba Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Tue, 17 Mar 2015 19:08:24 -0400
Subject: [PATCH 14/16] checkdoc round 2

---
 doi-utils.el | 78 ++++++++++++++++++++++++++++++++++++----------------
 1 file changed, 55 insertions(+), 23 deletions(-)

diff --git a/doi-utils.el b/doi-utils.el
index 4e80d16..e3e8b94 100644
--- a/doi-utils.el
+++ b/doi-utils.el
@@ -47,7 +47,8 @@
   "Stores redirect url from a callback function.")
 
 (defun doi-utils-redirect-callback (&optional status)
-  "Callback for url-retrieve to set the redirect."
+  "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
@@ -84,6 +85,7 @@
 ;; ** 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*)))
 
@@ -91,6 +93,7 @@
 ;; ** 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")))
 
@@ -98,6 +101,7 @@
 ;; ** 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))
@@ -117,7 +121,8 @@
 
 (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."
+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)
@@ -129,6 +134,7 @@ We get it out here by parsing the html."
   *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*))
@@ -138,6 +144,7 @@ We get it out here by parsing the html."
 ;; ** Springer
 
 (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"))))
 
@@ -149,6 +156,7 @@ We get it out here by parsing the html."
 ;; we just change /abs/ to /pdf/.
 
 (defun acs-pdf-url (*doi-utils-redirect*)
+  "Get url to the pdf from *DOI-UTILS-REDIRECT*."
   (when (string-match "^http://pubs.acs.org" *doi-utils-redirect*)
     (replace-regexp-in-string "/abs/" "/pdf/" *doi-utils-redirect*)))
 
@@ -156,6 +164,7 @@ We get it out here by parsing the html."
 ;; ** 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*)))
@@ -166,6 +175,7 @@ We get it out here by parsing the html."
 ;; ** 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")))
 
@@ -173,10 +183,12 @@ We get it out here by parsing the html."
 ;; ** 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 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)))
@@ -186,12 +198,14 @@ We get it out here by parsing the html."
 ;; ** 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*)))
 
@@ -200,6 +214,7 @@ We get it out here by parsing the html."
 
 
 (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")))
 
@@ -208,6 +223,7 @@ We get it out here by parsing the html."
 ;; ** 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))
@@ -217,10 +233,11 @@ We get it out here by parsing the html."
 ;; 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")
+  "Stores url to pdf download from a callback function.")
 
 (defun doi-utils-get-science-direct-pdf-url (redirect-url)
-  "Science direct hides the pdf url in html. we get it out here."
+  "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)
@@ -233,6 +250,7 @@ We get it out here by parsing the html."
 
 
 (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*))
@@ -242,7 +260,9 @@ We get it out here by parsing the html."
 ;; which actually redirect to
 ;; http://www.sciencedirect.com/science/article/pii/S0927025609004558
 (defun linkinghub-elsevier-pdf-url (*doi-utils-redirect*)
-  (when (string-match "^http://linkinghub.elsevier.com/retrieve" *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"
@@ -258,6 +278,7 @@ We get it out here by parsing the html."
 ;; 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")))
 
@@ -288,7 +309,7 @@ We get it out here by parsing the html."
 (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"
+until one is found."
   (doi-utils-get-redirect doi)
 
   (unless *doi-utils-redirect*
@@ -374,7 +395,7 @@ at the end."
 
 
 (defun doi-utils-expand-template (s)
-  "Expand a template containing %{} with the eval of its contents."
+  "Expand a string template S containing %{} with the eval of its contents."
   (replace-regexp-in-string "%{\\([^}]+\\)}"
                             (lambda (arg)
                               (let ((sexp (substring arg 2 -1)))
@@ -410,10 +431,12 @@ at the end."
 (setq doi-utils-bibtex-type-generators nil)
 
 (defun doi-utils-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,
+  "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."
+without changing the results.  ACC is the list of additional
+expressions."
   (cond ((null lst) (nreverse acc))
         ((and (stringp (car lst))
               (stringp (car acc)))
@@ -422,15 +445,19 @@ without changing the results."
         (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' with
-`fields' (given as symbols), matching to retrieval expressions in
-`doi-utils-json-metadata-extract'. This type will only be used
+  "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."
+MATCHING-TYPES - a list of strings."
   `(push (lambda (type results)
-           (when (or ,@(mapcar (lambda (match-type) `(string= type ,match-type)) matching-types))
+           (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)))
+                             (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)))
@@ -546,7 +573,8 @@ prompt. Otherwise, you have to type or pste in a DOI."
 
 
 (defun bibtex-set-field (field value &optional nodelim)
-  "Set FIELD to VALUE in bibtex file. create field if it does not exist."
+  "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))
@@ -667,7 +695,8 @@ Data is retrieved from the doi in the entry."
     "http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:doi/%s" doi)))
 
 (defun doi-utils-wos-citing (doi)
-  "Open Web of Science citing articles entry. May be empty if none are found."
+  "Open Web of Science citing articles entry for DOI.
+May be empty if none are found."
   (interactive "sDOI: ")
   (browse-url
    (concat
@@ -676,7 +705,7 @@ Data is retrieved from the doi in the entry."
     "&svc_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Asch_svc&svc.citing=yes")))
 
 (defun doi-utils-wos-related (doi)
-  "Open Web of Science related articles page."
+  "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"
@@ -697,6 +726,7 @@ Data is retrieved from the doi in the entry."
 
 
 (defun doi-utils-open (doi)
+  "Open DOI in browser."
  (interactive "sDOI: ")
  (browse-url (concat "http://dx.doi.org/" doi)))
 
@@ -738,8 +768,9 @@ Data is retrieved from the doi in the entry."
 
 
 (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.")
+ "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)
@@ -755,7 +786,8 @@ The function must take one argument, the doi.")
 
 (defun doi-link-menu (link-string)
    "Generate the link menu message, get choice and execute it.
-Options are stored in `doi-link-menu-funcs'."
+Options are stored in `doi-link-menu-funcs'.
+Argument LINK-STRING Passed in on link click."
    (interactive)
    (message
    (concat
-- 
2.39.2


From e8e9831beeb3f43fcf57483f8fd4efc63deb1261 Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Tue, 17 Mar 2015 19:27:45 -0400
Subject: [PATCH 15/16] fix issue #24

https://github.com/jkitchin/org-ref/issues/24
I put a save-restriction/widen wrapper around the link message to make sure it can find the bibfile, or other information it needs.
---
 org-ref.el | 159 +++++++++++++++++++++++++++--------------------------
 1 file changed, 80 insertions(+), 79 deletions(-)

diff --git a/org-ref.el b/org-ref.el
index 86d2464..3fdecfb 100644
--- a/org-ref.el
+++ b/org-ref.el
@@ -2845,87 +2845,88 @@ Shows bad citations, ref links and labels"
 (defun org-ref-link-message ()
   "Print a minibuffer message about the link that point is on."
   (interactive)
-  (when (eq major-mode 'org-mode)
-    (let* ((object (org-element-context))
-	   (type (org-element-property :type object)))
-      (save-excursion
-	(cond
-	 ;; cite links
-	 ((-contains? org-ref-cite-types type)
-	  (message (org-ref-get-citation-string-at-point)))
-
-	 ;; message some context about the label we are referring to
-	 ((string= type "ref")
-	  (message "%scount: %s"
-		   (org-ref-get-label-context
-		    (org-element-property :path object))
-		   (org-ref-count-labels
-			(org-element-property :path object))))
-
-	 ((string= type "eqref")
-	  (message "%scount: %s"
-		   (org-ref-get-label-context
-		    (org-element-property :path object))
-		   (org-ref-count-labels
-			(org-element-property :path object))))
-
-	 ;; message the count
-	 ((string= type "label")
-	  (let ((count (org-ref-count-labels
-			(org-element-property :path object))))
-	    ;; get plurality on occurrence correct
-	    (message (concat
-		      (number-to-string count)
-		      " occurence"
-		      (when (or (= count 0)
-				(> count 1))
-			"s")))))
-
-	 ((string= type "custom-id")
-	  (save-excursion
-	    (org-open-link-from-string
-	     (format "[[#%s]]" (org-element-property :path object)))
-	    (message "%s" (org-get-heading))))
-
-         ;; check if the bibliography files exist.
-	 ((string= type "bibliography")
-	  (let* ((bibfile)
-		 ;; object is the link you clicked on
-		 (object (org-element-context))
-		 (link-string (org-element-property :path object))
-		 (link-string-beginning)
-		 (link-string-end))
-	    (save-excursion
-	      (goto-char (org-element-property :begin object))
-	      (search-forward link-string nil nil 1)
-	      (setq link-string-beginning (match-beginning 0))
-	      (setq link-string-end (match-end 0)))
-
-	     ;; make sure we are in link and not before the :
-	    (when (> link-string-beginning (point))
-	      (goto-char link-string-beginning))
-
-	    ;; now if we have comma separated bibliographies
-	    ;; we find the one clicked on. we want to
-	    ;; search forward to next comma from point
+  (save-restriction
+    (widen)
+    (when (eq major-mode 'org-mode)
+      (let* ((object (org-element-context))
+	     (type (org-element-property :type object)))
+	(save-excursion
+	  (cond
+	   ;; cite links
+	   ((-contains? org-ref-cite-types type)
+	    (message (org-ref-get-citation-string-at-point)))
+
+	   ;; message some context about the label we are referring to
+	   ((string= type "ref")
+	    (message "%scount: %s"
+		     (org-ref-get-label-context
+		      (org-element-property :path object))
+		     (org-ref-count-labels
+		      (org-element-property :path object))))
+
+	   ((string= type "eqref")
+	    (message "%scount: %s"
+		     (org-ref-get-label-context
+		      (org-element-property :path object))
+		     (org-ref-count-labels
+		      (org-element-property :path object))))
+
+	   ;; message the count
+	   ((string= type "label")
+	    (let ((count (org-ref-count-labels
+			  (org-element-property :path object))))
+	      ;; get plurality on occurrence correct
+	      (message (concat
+			(number-to-string count)
+			" occurence"
+			(when (or (= count 0)
+				  (> count 1))
+			  "s")))))
+
+	   ((string= type "custom-id")
 	    (save-excursion
-	      (if (search-forward "," link-string-end 1 1)
-		  (setq key-end (- (match-end 0) 1)) ; we found a match
-		(setq key-end (point)))) ; no comma found so take the point
+	      (org-open-link-from-string
+	       (format "[[#%s]]" (org-element-property :path object)))
+	      (message "%s" (org-get-heading))))
+
+	   ;; check if the bibliography files exist.
+	   ((string= type "bibliography")
+	    (let* ((bibfile)
+		   ;; object is the link you clicked on
+		   (object (org-element-context))
+		   (link-string (org-element-property :path object))
+		   (link-string-beginning)
+		   (link-string-end))
+	      (save-excursion
+		(goto-char (org-element-property :begin object))
+		(search-forward link-string nil nil 1)
+		(setq link-string-beginning (match-beginning 0))
+		(setq link-string-end (match-end 0)))
+
+	      ;; make sure we are in link and not before the :
+	      (when (> link-string-beginning (point))
+		(goto-char link-string-beginning))
+
+	      ;; now if we have comma separated bibliographies
+	      ;; we find the one clicked on. we want to
+	      ;; search forward to next comma from point
+	      (save-excursion
+		(if (search-forward "," link-string-end 1 1)
+		    (setq key-end (- (match-end 0) 1)) ; we found a match
+		  (setq key-end (point)))) ; no comma found so take the point
 
-	    ;; and backward to previous comma from point
-	    (save-excursion
-	      (if (search-backward "," link-string-beginning 1 1)
-		  (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
-		(setq key-beginning (point)))) ; no match found
-	    ;; save the key we clicked on.
-	    (setq bibfile
-		  (org-ref-strip-string
-		   (buffer-substring key-beginning key-end)))
-	    (if (file-exists-p bibfile)
-		(message "%s exists." bibfile)
-	      (message "!!! %s NOT FOUND !!!" bibfile))))
-	 )))))
+	      ;; and backward to previous comma from point
+	      (save-excursion
+		(if (search-backward "," link-string-beginning 1 1)
+		    (setq key-beginning (+ (match-beginning 0) 1)) ; we found a match
+		  (setq key-beginning (point)))) ; no match found
+	      ;; save the key we clicked on.
+	      (setq bibfile
+		    (org-ref-strip-string
+		     (buffer-substring key-beginning key-end)))
+	      (if (file-exists-p bibfile)
+		  (message "%s exists." bibfile)
+		(message "!!! %s NOT FOUND !!!" bibfile))))))))))
 
 ;; ** aliases
 (defalias 'oro 'org-ref-open-citation-at-point)
-- 
2.39.2


From 48088ad943d71bf13541140b628b2a8aed1d31db Mon Sep 17 00:00:00 2001
From: John Kitchin <jkitchin@andrew.cmu.edu>
Date: Tue, 17 Mar 2015 19:29:12 -0400
Subject: [PATCH 16/16] another minor tweak of cite express regexp

I found an odd key with / in it. that is covered now.
---
 org-ref.el | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/org-ref.el b/org-ref.el
index 3fdecfb..248a417 100644
--- a/org-ref.el
+++ b/org-ref.el
@@ -326,7 +326,7 @@ You will see a message in the minibuffer when on a cite, ref or label link."
 		       (replace-regexp-in-string "\*" "\\\\*" x)
 		       )
 		     org-ref-cite-types "\\|") "\\)"
-  ":\\([a-zA-Z0-9-_:\\.]*,?\\)*"))
+  ":\\([a-zA-Z0-9-_:\\./]*,?\\)*"))
 
 
 (setq org-ref-label-re
-- 
2.39.2