(feat): fix citation links not showing up in graph (#547)

This change adds a `type` column to the refs column, and strips the prefix before storing the key in the `refs` table.

CHANGELOG.md

@@ -4,12 +4,15 @@
 
 ### Breaking Changes
 * [#523](https://github.com/jethrokuan/org-roam/pull/523) remove `org-roam-completion-fuzzy-match` in favor of using completion mechanism's configuration options directly 
+* [#547](https://github.com/jethrokuan/org-roam/pull/547) Deprecate `org-roam-db--maybe-update`, in favour of `org-roam-db--update-maybe`.
+* [#547](https://github.com/jethrokuan/org-roam/pull/547) Added `type` column to the `refs` table.
 
 ### Bugfixes
 * [#509](https://github.com/jethrokuan/org-roam/pull/509) fix backup files being tracked in database
 * [#509](https://github.com/jethrokuan/org-roam/pull/509) fix external org files being tracked in database
 * [#537](https://github.com/jethrokuan/org-roam/pull/537) quote graphviz node and edge configuration options to allow multi-word configurations
 * [#545](https://github.com/jethrokuan/org-roam/pull/545) fix `org-roam--extract-links` to ensure that multiple citations (`cite:key1,key2`) are split correctly
+* [#547](https://github.com/jethrokuan/org-roam/pull/547) Fix unlinked citations.
 
 ### Features
 * [#538](https://github.com/jethrokuan/org-roam/pull/538) Optionally use text in first headline as title

org-roam-buffer.el

@@ -114,14 +114,11 @@ When non-nil, the window will not be closed when deleting other windows."
 
 (defun org-roam-buffer--insert-citelinks ()
   "Insert citation backlinks for the current buffer."
-  (if-let* ((roam-key (with-temp-buffer
+  (if-let* ((ref (with-temp-buffer
-                        (insert-buffer-substring org-roam-buffer--current)
+                   (insert-buffer-substring org-roam-buffer--current)
-                        (org-roam--extract-ref)))
+                   (org-roam--extract-ref)))
             (org-ref-p (require 'org-ref nil t)) ; Ensure that org-ref is present
-            (cite-prefixes (-map (lambda (type)
+            (key-backlinks (org-roam--get-backlinks (cdr ref)))
-                                   (concat type ":")) org-ref-cite-types))
-            (key-backlinks (org-roam--get-backlinks
-                            (s-chop-prefixes cite-prefixes roam-key)))
             (grouped-backlinks (--group-by (nth 0 it) key-backlinks)))
       (progn
         (insert (let ((l (length key-backlinks)))
@@ -196,6 +193,7 @@ When non-nil, the window will not be closed when deleting other windows."
         (run-hooks 'org-roam-buffer-prepare-hook)
         (read-only-mode 1)))))
 
+
 (cl-defun org-roam-buffer--update-maybe (&key redisplay)
   "Reconstructs `org-roam-buffer'.
 This needs to be quick or infrequent, because this is run at

org-roam-compat.el

@@ -77,6 +77,8 @@
   "org-roam 1.1.0")
 (define-obsolete-function-alias 'org-roam--capture 'org-roam-capture--capture
   "org-roam 1.1.0")
+(define-obsolete-function-alias 'org-roam-db--maybe-update 'org-roam-db--update-maybe
+  "org-roam 1.1.0")
 
 ;;;; Variables
 (define-obsolete-variable-alias 'org-roam-graphviz-extra-options

org-roam-db.el

@@ -56,7 +56,7 @@ when used with multiple Org-roam instances."
   :type 'string
   :group 'org-roam)
 
-(defconst org-roam-db--version 2)
+(defconst org-roam-db--version 3)
 (defconst org-roam-db--sqlite-available-p
   (with-demoted-errors "Org-roam initialization: %S"
     (emacsql-sqlite-ensure-binary)
@@ -94,7 +94,7 @@ Performs a database upgrade when required."
         (when init-db
           (org-roam-db--init conn))
         (let* ((version (caar (emacsql conn "PRAGMA user_version")))
-               (version (org-roam-db--maybe-update conn version)))
+               (version (org-roam-db--update-maybe conn version)))
           (cond
            ((> version org-roam-db--version)
             (emacsql-close conn)
@@ -134,7 +134,8 @@ SQL can be either the emacsql vector representation, or a string."
 
     (refs
      [(ref :unique :not-null)
-      (file :not-null)])))
+      (file :not-null)
+      (type :not-null)])))
 
 (defun org-roam-db--init (db)
   "Initialize database DB with the correct schema and user version."
@@ -143,16 +144,16 @@ SQL can be either the emacsql vector representation, or a string."
       (emacsql db [:create-table $i1 $S2] table schema))
     (emacsql db (format "PRAGMA user_version = %s" org-roam-db--version))))
 
-(defun org-roam-db--maybe-update (db version)
+(defun org-roam-db--update-maybe (db version)
   "Upgrades the database schema for DB, if VERSION is old."
   (emacsql-with-transaction db
     'ignore
-    (when (= version 1)
+    (if (< version org-roam-db--version)
-      (progn
+        (progn
-        (warn "No good way to perform a DB upgrade, rebuilding from scratch...")
+          (message (format "Upgrading the Org-roam database from version %d to version %d"
-        (delete-file (org-roam-db--get))
+                           version org-roam-db--version))
-        (org-roam-db-build-cache)))
+          (org-roam-db-build-cache t))))
-    version))
+  version)
 
 (defun org-roam-db--close (&optional db)
   "Closes the database connection for database DB.
@@ -228,10 +229,11 @@ This is equivalent to removing the node from the graph."
 
 (defun org-roam-db--insert-ref (file ref)
   "Insert REF for FILE into the Org-roam cache."
-  (org-roam-db-query
+  (let ((key (cdr ref))
-   [:insert :into refs
+        (type (car ref)))
-    :values $v1]
+    (org-roam-db-query
-   (list (vector ref file))))
+     [:insert :into refs :values $v1]
+     (list (vector key file type)))))
 
 ;;;;; Fetching
 (defun org-roam-db--get-current-files ()
@@ -368,8 +370,10 @@ If FORCE, force a rebuild of the cache from scratch."
               (setq all-links (append links all-links)))
             (let ((titles (org-roam--extract-and-format-titles file)))
               (setq all-titles (cons (vector file titles) all-titles)))
-            (when-let ((ref (org-roam--extract-ref)))
+            (when-let* ((ref (org-roam--extract-ref))
-              (setq all-refs (cons (vector ref file) all-refs))))
+                        (type (car ref))
+                        (key (cdr ref)))
+              (setq all-refs (cons (vector key file type) all-refs))))
           (remhash file current-files))))
     (dolist (file (hash-table-keys current-files))
       ;; These files are no longer around, remove from cache...

org-roam-graph.el

@@ -173,7 +173,8 @@ into a digraph."
             `[:with selected :as [:select [file] :from ,node-query]
               :select :distinct [file from]
               :from links :inner :join refs :on (and (= links:to refs:ref)
-                                                     (= links:type "cite"))
+                                                     (= links:type "cite")
+                                                     (= refs:type "cite"))
               :where (and (in file selected) (in from selected))])
            (edges       (org-roam-db-query edges-query))
            (edges-cites (org-roam-db-query edges-cites-query)))

org-roam.el

@@ -375,9 +375,44 @@ current buffer is used."
             (org-roam--format-title title file-path))
           (org-roam--extract-titles)))
 
+(defun org-roam--ref-type-p (type)
+  "Return t if the ref from current buffer is TYPE."
+  (let ((current (car (org-roam--extract-ref))))
+    (eq current type)))
+
 (defun org-roam--extract-ref ()
-  "Extract the ref from current buffer."
+  "Extract the ref from current buffer and return the type and the key of the ref."
-  (cdr (assoc "ROAM_KEY" (org-roam--extract-global-props '("ROAM_KEY")))))
+  (if-let ((ref (cdr (assoc "ROAM_KEY" (org-roam--extract-global-props '("ROAM_KEY"))))))
+      (let* ((type (org-roam--ref-type ref))
+             (key (cond ((string= "cite" type)
+                         (s-chop-prefix (org-roam--cite-prefix ref) ref))
+                        (t ref))))
+        (cons type key))
+    nil))
+
+(defun org-roam--ref-type (ref)
+  "Determine the type of the REF from the prefix."
+  (let* ((cite-prefix (org-roam--cite-prefix ref))
+         (is-website (seq-some
+                      (lambda (prefix) (s-prefix? prefix ref))
+                      '("http" "https")))
+         (type (cond (cite-prefix "cite")
+                     (is-website "website")
+                     (t "roam"))))
+    type))
+
+(defun org-roam--cite-prefix (ref)
+  "Return the citation prefix of REF, or nil otherwise.
+The prefixes are defined in `org-ref-cite-types`.
+Examples:
+   (org-roam--cite-prefix \"cite:foo\") -> \"cite:\"
+   (org-roam--cite-prefix \"https://google.com\") -> nil"
+  (when (require 'org-ref nil t)
+   (seq-find
+    (lambda (prefix) (s-prefix? prefix ref))
+    (-map (lambda (type) (concat type ":"))
+          org-ref-cite-types))))
+
 ;;;; Title/Path/Slug conversion
 (defun org-roam--path-to-slug (path)
   "Return a slug from PATH."
@@ -555,18 +590,37 @@ command will offer you to create one."
       (when (y-or-n-p "Index file does not exist.  Would you like to create it? ")
         (org-roam-find-file "Index")))))
 
-(defun org-roam--get-ref-path-completions ()
+;;;; org-roam-find-ref
-  "Return a list of cons pairs for refs to absolute path of Org-roam files."
+(defcustom org-roam-include-type-in-ref-path-completions nil
-  (let ((rows (org-roam-db-query [:select [ref file] :from refs])))
+  "When t, include the type in ref-path completions.
-    (mapcar (lambda (row)
+Note that this only affects interactive calls.
-              (cons (car row)
+See `org-roam--get-ref-path-completions' for details."
-                    (cadr row))) rows)))
+  :type 'boolean
+  :group 'org-roam)
 
-(defun org-roam-find-ref (&optional info)
+(defun org-roam--get-ref-path-completions (&optional interactive)
+  "Return a list of cons pairs for refs to absolute path of Org-roam files.
+When INTERACTIVE `org-roam-include-type-in-ref-path-completions'
+are non-nil, format the car of the completion-candidates as
+'type:ref'."
+  (let ((rows (org-roam-db-query [:select [type ref file] :from refs]))
+        (include-type (and interactive
+                           org-roam-include-type-in-ref-path-completions)))
+    (mapcar (lambda (row)
+              (cl-destructuring-bind (type ref file) row
+                (cons (if include-type
+                          (format "%s:%s" type ref)
+                        ref)
+                      file)))
+            rows)))
+
+(defun org-roam-find-ref (arg &optional info)
   "Find and open an Org-roam file from a ref.
-INFO is an alist containing additional information."
+INFO is an alist containing additional information.
-  (interactive)
+ARG is used to forward interactive calls to
-  (let* ((completions (org-roam--get-ref-path-completions))
+`org-roam--get-ref-path-completions'"
+  (interactive "p")
+  (let* ((completions (org-roam--get-ref-path-completions arg))
          (ref (or (cdr (assoc 'ref info))
                   (org-roam-completion--completing-read "Ref: "
                                                         completions
@@ -658,7 +712,7 @@ file."
     (define-key map [mouse-1] 'org-open-at-point)
     (define-key map (kbd "RET") 'org-open-at-point)
     map)
-  "Keymap for `org-roam-backlinks-mode'.")
+  "Keymap for symbol `org-roam-backlinks-mode'.")
 
 (define-minor-mode org-roam-backlinks-mode
   "Minor mode for the `org-roam-buffer'.
@@ -731,7 +785,7 @@ for Org-ref cite links."
 ;;; The global minor org-roam-mode
 (defvar org-roam-mode-map
   (make-sparse-keymap)
-  "Keymap for mode `org-roam-mode'.")
+  "Keymap for mode symbol `org-roam-mode'.")
 
 ;;;###autoload
 (define-minor-mode org-roam-mode
@@ -755,11 +809,11 @@ Otherwise, behave as if called interactively."
   :global t
   (cond
    (org-roam-mode
-    (org-roam-db-build-cache)
     (add-hook 'find-file-hook #'org-roam--find-file-hook-function)
     (add-hook 'kill-emacs-hook #'org-roam-db--close-all)
     (advice-add 'rename-file :after #'org-roam--rename-file-advice)
-    (advice-add 'delete-file :before #'org-roam--delete-file-advice))
+    (advice-add 'delete-file :before #'org-roam--delete-file-advice)
+    (org-roam-db-build-cache))
    (t
     (remove-hook 'find-file-hook #'org-roam--find-file-hook-function)
     (remove-hook 'kill-emacs-hook #'org-roam-db--close-all)
@@ -774,7 +828,7 @@ Otherwise, behave as if called interactively."
         (remove-hook 'after-save-hook #'org-roam-db--update-file t))))))
 
 (defun org-roam--find-file-hook-function ()
-  "Called by `find-file-hook' when mode `org-roam-mode' is on."
+  "Called by `find-file-hook' when mode symbol `org-roam-mode' is on."
   (when (org-roam--org-roam-file-p)
     (setq org-roam-last-window (get-buffer-window))
     (add-hook 'post-command-hook #'org-roam-buffer--update-maybe nil t)

tests/test-org-roam.el

@@ -107,7 +107,7 @@
 
     (expect (org-roam-db-query [:select * :from refs])
             :to-have-same-items-as
-            (list (list "https://google.com/" (org-roam-test-abs-path "web_ref.org"))))
+            (list (list "https://google.com/" (org-roam-test-abs-path "web_ref.org") "website")))
 
     ;; Expect rebuilds to be really quick (nothing changed)
     (expect (org-roam-db-build-cache)
@@ -299,7 +299,7 @@
   (it "delete web_ref"
     (expect (org-roam-db-query [:select * :from refs])
             :to-have-same-items-as
-            (list (list "https://google.com/" (org-roam-test-abs-path "web_ref.org"))))
+            (list (list "https://google.com/" (org-roam-test-abs-path "web_ref.org") "website")))
     (delete-file (org-roam-test-abs-path "web_ref.org"))
     (expect (org-roam-db-query [:select * :from refs])
             :to-have-same-items-as