From 8de55eca2804a0d50af33c273b69bdddb5c111d5 Mon Sep 17 00:00:00 2001
From: Kyle Meyer <kyle@kyleam.com>
Date: Thu, 11 Dec 2014 23:18:30 -0500
Subject: Add command to list orphan citekeys

---
 NEWS     |  3 +++
 bog-todo |  2 +-
 bog.el   | 45 +++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 49 insertions(+), 1 deletion(-)

diff --git a/NEWS b/NEWS
index dbef01f..c11a25c 100644
--- a/NEWS
+++ b/NEWS
@@ -34,6 +34,9 @@
 - New commands =bog-next-non-heading-citekey= and
   =bog-previous-non-heading-citekey=
 
+- New command =bog-list-orphan-citekeys= finds citekeys that are
+  referred to in the notes but don't have their own heading.
+
 ** Other changes
 
 - =bog-goto-citekey-heading-in-buffer= and
diff --git a/bog-todo b/bog-todo
index 785ae48..7309776 100644
--- a/bog-todo
+++ b/bog-todo
@@ -24,7 +24,7 @@ Perhaps use a cache file.  This could be used in
 
 * Notes
 
-** ENH Find in-text citekeys that don't have a header
+** DONE Find in-text citekeys that don't have a header
 
 ** CANCELED Check for duplicate citekeys headings
    :LOGBOOK:
diff --git a/bog.el b/bog.el
index 4207855..dc4899d 100644
--- a/bog.el
+++ b/bog.el
@@ -345,6 +345,44 @@ word constituents."
   (--keep it
           (org-map-entries 'bog-citekey-from-heading nil 'file)))
 
+(defun bog-non-heading-citekeys-in-file (file)
+  "Return all non-heading citekeys in FILE."
+  (let (refs
+        case-fold-search)
+    (with-temp-buffer
+      (org-mode)
+      (insert-file-contents file)
+      (while (re-search-forward bog-citekey-format nil t)
+        (unless (or (org-at-heading-p)
+                    (org-at-property-p))
+          (push (match-string-no-properties 0) refs))))
+    (-distinct refs)))
+
+(defun bog-list-orphan-citekeys (&optional file)
+  "List in citekeys that appear in notes but don't have heading.
+With prefix FILE, include only orphan citekeys from that file."
+  (interactive (list (and current-prefix-arg
+                          (bog-read-note-file-name))))
+  (let ((files (or (and file (list file))
+                   (bog-notes)))
+        (heading-cks (bog-all-heading-citekeys))
+        cks)
+    (with-current-buffer (get-buffer-create "*Bog orphan citekeys*")
+      (delete-region (point-min) (point-max))
+      (insert "\n")
+      (-each files
+        (lambda (f)
+          (setq cks
+                (--> (bog-non-heading-citekeys-in-file f)
+                  (-difference it heading-cks)
+                  (-sort (lambda (x y) (string-lessp x y)) it)
+                  (mapconcat #'identity it "\n")))
+          (unless (equal cks "")
+            (insert (format "* %s\n\n" (file-name-nondirectory f)))
+            (insert (concat cks "\n\n")))))
+      (org-mode)
+      (show-all))))
+
 
 ;;; Citekey-associated files
 
@@ -740,6 +778,13 @@ level `bog-refile-maxlevel' are considered."
     (concat (file-name-as-directory bog-note-directory)
             "*.org"))))
 
+(defun bog-read-note-file-name ()
+  (let ((nodir-files (-annotate #'file-name-nondirectory
+                                (bog-notes))))
+    (cdr (assoc (org-icompleting-read "File: "
+                                      (-map #'car nodir-files))
+                nodir-files))))
+
 (defun bog-search-notes (&optional todo-only string)
   "Search notes using `org-search-view'.
 With prefix argument TODO-ONLY, only TODO entries are searched.
-- 
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