X-Git-Url: https://git.donarmstrong.com/?p=org-ref.git;a=blobdiff_plain;f=org-ref.org;h=c59d8d10b60b79c78f03b16d84479a6a6767af02;hp=ae39ab90db19d312ce8300a99a63dfab005434f9;hb=1640b223fedc30e829bea58d949881d27894b572;hpb=9afe00c1615fd24ee658620990ac03448279f04a

diff --git a/org-ref.org b/org-ref.org
index ae39ab9..c59d8d1 100644
--- a/org-ref.org
+++ b/org-ref.org
@@ -218,11 +218,35 @@ We setup reftex here. We use a custom insert cite link function defined here: [[
 	 ;; I do not remember why I put this next line in. It doesn't
 	 ;; work for org-files. Nothing very bad happens, but it gives
 	 ;; an annoying error. Commenting it out for now.
-         ;(reftex-parse-all)
+         ;(reftex-parse-all
 	 )
     (make-local-variable 'reftex-cite-format)
-    (setq reftex-cite-format 'org)
-    (define-key org-mode-map (kbd org-ref-insert-cite-key) org-ref-insert-cite-function))
+    (setq reftex-cite-format 'org))
+
+;; define key for inserting citations
+(define-key org-mode-map
+  (kbd org-ref-insert-cite-key)
+  org-ref-insert-cite-function)
+
+(when org-ref-show-citation-on-enter
+ (setq org-ref-message-timer
+       (run-with-idle-timer 0.5 t 'org-ref-link-message)))
+
+(defun org-ref-show-link-messages ()
+  "Turn on link messages. You will see a message in the
+minibuffer when on a cite, ref or label link."
+  (interactive)
+  (setq org-ref-message-timer
+	(run-with-idle-timer 0.5 t 'org-ref-link-message))
+  )
+(defun org-ref-cancel-link-messages ()
+  "Stop showing messages in minibuffer when on a link."
+  (interactive)
+  (cancel-timer org-ref-message-timer))
+
+;; this approach caused the selected region to not be highlighted any more.
+; (add-hook 'post-command-hook 'org-ref-link-message))
+; (remove-hook 'post-command-hook 'org-ref-link-message))
 
 (add-hook 'org-mode-hook 'org-mode-reftex-setup)
 
@@ -2023,7 +2047,6 @@ And at the end of the document put \makeglossaries.
 #+END_SRC
 
 
-
 * Utilities
 ** create simple text citation from bibtex entry
 
@@ -2652,11 +2675,8 @@ Sometimes it may be helpful to manually change the order of citations. These fun
 (add-hook 'org-shiftleft-hook (lambda () (org-ref-swap-citation-link -1)))
 #+END_SRC
 
-
 ** Lightweight messages about links
-To get a lighter weight message about the label, ref and cite links, we define a function that gives us the minibuffer message, without the menu. We add it to a hook that updates after every command, including cursor movements.
-
-ref:test citep:test  label:rett
+To get a lighter weight message about the label, ref and cite links, we define a function that gives us the minibuffer message, without the menu. We run this in an idle timer.
 
 #+BEGIN_SRC emacs-lisp :tangle org-ref.el
 (defun org-ref-get-label-context (label)
@@ -2666,17 +2686,38 @@ ref:test citep:test  label:rett
       (goto-char (point-min))
       (when (re-search-forward
 	     (format "label:%s\\b" label) nil t)
-	(throw 'result (thing-at-point 'paragraph)))
+	(throw 'result (buffer-substring
+			(progn
+			  (previous-line)
+			  (beginning-of-line)
+			  (point))
+			(progn
+			  (forward-line 4)
+			  (point)))))
 
       (goto-char (point-min))
       (when (re-search-forward
 	     (format "\\label{%s}" label) nil t)
-	(throw 'result  (thing-at-point 'paragraph)))
+	(throw 'result (buffer-substring
+			(progn
+			  (previous-line)
+			  (beginning-of-line)
+			  (point))
+			(progn
+			  (forward-line 4)
+			  (point)))))
 
       (goto-char (point-min))
       (when (re-search-forward
 	     (format "^#\\+label:\\s-*\\(%s\\)\\b" label) nil t)
-	(throw 'result (thing-at-point 'paragraph)))
+	(throw 'result (buffer-substring
+			(progn
+			  (previous-line)
+			  (beginning-of-line)
+			  (point))
+			(progn
+			  (forward-line 4)
+			  (point)))))
 
       (goto-char (point-min))
       (when (re-search-forward
@@ -2690,36 +2731,39 @@ ref:test citep:test  label:rett
 			  (forward-line 4)
 			  (point))))))))
 
+
 (defun org-ref-link-message ()
   "Print a minibuffer message about the link that point is on."
   (interactive)
-  (let* ((object (org-element-context))
-	 (type (org-element-property :type object)))
+  (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)))
 
-    (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-box "%s" (org-element-property :path object))
-      (message (org-ref-get-label-context
-		(org-element-property :path object))))
-
-     ;; message the count
-     ((string= type "label")
-      (let ((count (org-ref-count-labels
+	 ;; message some context about the label we are referring to
+	 ((string= type "ref")
+	  (message (org-ref-get-label-context
 		    (org-element-property :path object))))
-	(message (concat
-		  (number-to-string count)
-		  " occurence"
-		  (when (or (= count 0)
-			    (> count 1))
-		    "s"))))))))
 
-(when org-ref-show-citation-on-enter
- (add-hook 'post-command-hook 'org-ref-link-message))
+	 ((string= type "eqref")
+	  (message (org-ref-get-label-context
+		    (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"))))))))))
 #+END_SRC
 
 * Aliases
@@ -2775,6 +2819,7 @@ Technically, this function should return a string that is inserted by helm. This
 	   (-contains?
 	    org-ref-cite-types
 	    (org-element-property :type object)))
+      ;;(message-box "in a link")
       (goto-char (org-element-property :end object))
       ;; sometimes there are spaces at the end of the link
       ;; this code moves point pack until no spaces are there
@@ -2782,26 +2827,31 @@ Technically, this function should return a string that is inserted by helm. This
       (insert (concat "," (mapconcat 'identity keys ","))))
 
      ;; We are next to a link, and we want to append
+     ;; next to a link means one character back is on a link.
      ((save-excursion
 	(backward-char)
 	(and (equal (org-element-type (org-element-context)) 'link)
 	     (-contains?
 	      org-ref-cite-types
 	      (org-element-property :type (org-element-context)))))
-      (goto-char (org-element-property :end object))
+      ;;(message-box "at end of a link")
+      ;; (goto-char (org-element-property :end object))
       (while (looking-back " ") (backward-char))
       (insert (concat "," (mapconcat 'identity keys ","))))
 
      ;; insert fresh link
      (t
+      ;;(message-box "fresh link")
       (insert
        (concat (if helm-current-prefix-arg
-                  (ido-completing-read "Type: " org-ref-cite-types)
+		   (helm :sources `((name . "link types")
+				    (candidates . ,org-ref-cite-types)
+				    (action . (lambda (x) x))))
                org-ref-default-citation-link)
 	       ":"
 	       (s-join "," keys))))))
-;; return empty string for helm
-"")
+  ;; return empty string for helm
+  "")
 
 (setq helm-bibtex-format-citation-functions
       '((org-mode . helm-bibtex-format-org-ref)))
@@ -2813,6 +2863,11 @@ Technically, this function should return a string that is inserted by helm. This
     (helm-bibtex)))
 
 (require 'helm-bibtex)
+
+(mapc (lambda (x) (add-to-list 'helm-bibtex-fallback-options x t))
+  '(("Crossref" . "http://search.crossref.org/?q=%s")
+    ("Scopus" . "http://www.scopus.com/scopus/search/submit/xadvanced.url?searchfield=TITLE-ABS-KEY(%s)")
+    ("Open Web of Science" . (lambda () (browse-url "http://apps.webofknowledge.com")))))
 #+END_SRC
 
 ** A helm click menu
@@ -2852,20 +2907,33 @@ Checks for pdf and doi, and add appropriate functions."
 		  (bibtex-autokey-get-field "doi"))))
 	 (candidates `(("Quit" . org-ref-citation-at-point)
 		       ("Open bibtex entry" . org-ref-open-citation-at-point))))
+    ;; for some reason, when there is no doi or url, they are returned as "". I
+    ;; prefer nil so we correct this here.
+    (when (string= doi "") (setq doi nil))
+    (when (string= url "") (setq url nil))
 
-
-    (when (file-exists-p pdf-file)
+    ;; Conditional pdf functions
+    (if (file-exists-p pdf-file)
+	(add-to-list
+	 'candidates
+	 '("Open pdf" . org-ref-open-pdf-at-point)
+	 t)
       (add-to-list
        'candidates
-       '("Open pdf" . org-ref-open-pdf-at-point)
-       t
-       ))
+       '("Try to get pdf" . (lambda ()
+			      (save-window-excursion
+				(org-ref-open-citation-at-point)
+                                (bibtex-beginning-of-entry)
+				(doi-utils-get-bibtex-entry-pdf))))
+       t))
+
 
     (add-to-list
      'candidates
      '("Open notes" . org-ref-open-notes-at-point)
      t)
 
+    ;; conditional url and doi functions
     (when (or url doi)
       (add-to-list
        'candidates