Rename to org-gnosis-ui & remove org-roam specific functions.

1 files changed, 235 insertions, 311 deletions

diff --git a/org-roam-ui.el b/org-gnosis-ui.el
index 775b3ea..84c10af 100644
--- a/org-roam-ui.el
+++ b/org-gnosis-ui.el
@@ -1,9 +1,11 @@
-;;; org-roam-ui.el --- User Interface for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
+;;; org-gnosis-ui.el --- User Interface for Org-Gnosis -*- coding: utf-8; lexical-binding: t; -*-
 
 ;; Copyright © 2021 Kirill Rogovoy, Thomas F. K. Jorna
+;; Copyright © 2024 Thanos Apollo
 
-;; author: Kirill Rogovoy, Thomas Jorna
-;; URL: https://github.com/org-roam/org-roam-ui
+;; author: Kirill Rogovoy, Thomas Jorna, Thanos Apollo
+;; Maintainer: Thanos Apollo <[email protected]>
+;; URL: https://git.thanosapollo.org/org-roam-ui/
 ;; Keywords: files outlines
 ;; Version: 0.1
 ;; Package-Requires: ((emacs "27.1") (simple-httpd "20191103.1446") (websocket "1.13"))
@@ -27,11 +29,12 @@
 
 ;;; Commentary:
 ;;
-;;  Org-roam-ui provides a web interface for navigating around notes created
-;;  within Org-roam.
+;;  org-gnosis-ui provides a web interface for navigating around notes created
+;;  within Org-gnosis.
 ;;
 ;;; Code:
 
+;;; Installing simple-httpd example:
 ;; (use-package simple-httpd
 ;;   :vc (:url "https://github.com/skeeto/emacs-web-server/"))
 
@@ -41,37 +44,37 @@
 (require 'org-gnosis)
 (require 'websocket)
 
-(defgroup org-roam-ui nil
+(defgroup org-gnosis-ui nil
   "UI in Org-roam."
-  :group 'org-roam-ui
-  :prefix "org-roam-ui-"
-  :link '(url-link :tag "Github" "https://github.com/org-roam/org-roam-ui"))
+  :group 'org-gnosis-ui
+  :prefix "org-gnosis-ui-"
+  :link '(url-link :tag "Github" "https://github.com/org-roam/org-gnosis-ui"))
 
-(defcustom org-roam-ui-directory org-gnosis-dir
-  "Directory of org-roam-ui notes."
-  :group 'org-roam-ui
+(defcustom org-gnosis-ui-directory org-gnosis-dir
+  "Directory of org-gnosis-ui notes."
+  :group 'org-gnosis-ui
   :type 'directory)
 
-(defcustom org-roam-ui-port 35902
+(defcustom org-gnosis-ui-port 35902
   "Roam UI Port."
-  :group 'org-roam-ui
+  :group 'org-gnosis-ui
   :type 'number)
 
-(defcustom org-roam-ui-sync-theme nil
-  "If true, sync your current Emacs theme with `org-roam-ui'.
+(defcustom org-gnosis-ui-sync-theme nil
+  "If true, sync your current Emacs theme with `org-gnosis-ui'.
 Works best with doom-themes.
-Ignored if a custom theme is provied for variable 'org-roam-ui-custom-theme'."
-  :group 'org-roam-ui
+Ignored if a custom theme is provied for variable `org-gnosis-ui-custom-theme'."
+  :group 'org-gnosis-ui
   :type 'boolean)
 
-(defcustom org-roam-ui-dailies-directory org-gnosis-journal-dir
+(defcustom org-gnosis-ui-dailies-directory org-gnosis-journal-dir
   "Dailies/Journaling directory."
-  :group 'org-roam-ui
+  :group 'org-gnosis-ui
   :type 'directory)
 
-(defcustom org-roam-ui-custom-theme nil
-  "Custom theme for `org-roam-ui'.
-Blocks 'org-roam-ui-sync-theme from syncing your current theme,
+(defcustom org-gnosis-ui-custom-theme nil
+  "Custom theme for `org-gnosis-ui'.
+Blocks 'org-gnosis-ui-sync-theme from syncing your current theme,
 instead sync this theme.
 Provide a list of cons with the following values:
 bg, bg-alt, fg, fg-alt, red, orange, yellow, green, cyan, blue, violet, magenta.
@@ -87,207 +90,216 @@ E.g. '((bg . \"#1E2029\")
 \(blue . \"#ff79c6\")
 \(violet . \"#8be9fd\")
 \(magenta . \"#bd93f9\"))."
-  :group 'org-roam-ui
+  :group 'org-gnosis-ui
   :type 'list)
 
-(defcustom org-roam-ui-follow t
-  "If true, `org-roam-ui' will follow you around in the graph."
-  :group 'org-roam-ui
+(defcustom org-gnosis-ui-follow t
+  "If true, `org-gnosis-ui' will follow you around in the graph."
+  :group 'org-gnosis-ui
   :type 'boolean)
 
-(defcustom org-roam-ui-update-on-save t
-  "If true, `org-roam-ui' will send new data when you save an `org-roam' buffer.
+(defcustom org-gnosis-ui-update-on-save t
+  "If true, `org-gnosis-ui' will send new data when you save an `org-roam' buffer.
 This can lead to some jank."
-  :group 'org-roam-ui
+  :group 'org-gnosis-ui
   :type 'boolean)
 
-(defcustom org-roam-ui-open-on-start t
-  "Whether to open your default browser when `org-roam-ui' launces."
-  :group 'org-roam-ui
+(defcustom org-gnosis-ui-open-on-start t
+  "Whether to open your default browser when `org-gnosis-ui' launces."
+  :group 'org-gnosis-ui
   :type 'boolean)
 
-(defcustom org-roam-ui-find-ref-title t
-  "Should `org-roam-ui' use `org-roam-bibtex' to find a reference's title?"
-  :group 'org-roam-ui
+(defcustom org-gnosis-ui-find-ref-title t
+  "Should `org-gnosis-ui' use `org-roam-bibtex' to find a reference's title?"
+  :group 'org-gnosis-ui
   :type 'boolean)
 
-(defcustom org-roam-ui-retitle-ref-nodes t
-  "Should `org-roam-ui' use `org-roam-bibtex' try to retitle reference nodes?"
-  :group 'org-roam-ui
+(defcustom org-gnosis-ui-retitle-ref-nodes t
+  "Should `org-gnosis-ui' use `org-roam-bibtex' try to retitle reference nodes?"
+  :group 'org-gnosis-ui
   :type 'boolean)
 
-(defcustom org-roam-ui-ref-title-template
+(defcustom org-gnosis-ui-ref-title-template
   "%^{author-abbrev} (%^{year}) %^{title}"
   "A template for title creation, used for references without associated nodes.
 
 This uses `orb--pre-expand-template' under the hood and therefore only org-style
 capture `%^{...}' are supported."
-  :group 'org-roam-ui
+  :group 'org-gnosis-ui
   :type 'string)
 
-(defcustom org-roam-ui-browser-function #'browse-url
-  "When non-nil launch org-roam-ui with a different browser function.
+(defcustom org-gnosis-ui-browser-function #'browse-url
+  "When non-nil launch org-gnosis-ui with a different browser function.
 Takes a function name, such as #'browse-url-chromium.
 Defaults to #'browse-url."
-  :group 'org-roam-ui
+  :group 'org-gnosis-ui
   :type 'function)
 
-(defcustom org-roam-ui-tags-function #'(lambda () (org-gnosis-select '* 'tags '1=1 t))
+(defcustom org-gnosis-ui-tags-function #'(lambda () (org-gnosis-select '* 'tags '1=1 t))
   "Function that returns all tags as a list."
-  :group 'org-roam-ui
+  :group 'org-gnosis-ui
   :type 'function)
 
-(defcustom org-roam-ui-nodes-function #'org-roam-ui-get-nodes
+(defcustom org-gnosis-ui-nodes-function #'org-gnosis-ui-get-nodes
   "Function that returns nodes."
-  :group 'org-roam-ui
+  :group 'org-gnosis-ui
   :type 'function)
 
-(defcustom org-roam-ui-links-function #'(lambda () (org-gnosis-select '* 'links))
+(defcustom org-gnosis-ui-node-query #'org-gnosis-ui-query
+  "Function that returns as ='(id file title level tag).
+
+Output of this function is then used by `org-gnosis-ui-get-nodes' to be
+formatted properly for json data."
+  :group 'org-gnosis-ui
+  :type 'function)
+
+(defcustom org-gnosis-ui-links-function #'(lambda () (org-gnosis-select '* 'links))
   "Function that returns links."
-  :group 'org-roam-ui
+  :group 'org-gnosis-ui
   :type 'function)
 
 ;;Hooks
 
-(defcustom org-roam-ui-before-open-node-functions nil
-  "Functions to run before a node is opened through org-roam-ui.
+(defcustom org-gnosis-ui-before-open-node-functions nil
+  "Functions to run before a node is opened through org-gnosis-ui.
 Take ID as string as sole argument."
-  :group 'org-roam-ui
+  :group 'org-gnosis-ui
   :type 'hook)
 
-(defcustom org-roam-ui-after-open-node-functions nil
-  "Functions to run after a node is opened through org-roam-ui.
+(defcustom org-gnosis-ui-after-open-node-functions nil
+  "Functions to run after a node is opened through org-gnosis-ui.
 Take ID as string as sole argument."
-  :group 'org-roam-ui
+  :group 'org-gnosis-ui
   :type 'hook)
 
-(defcustom org-roam-ui-latex-macros nil
-  "Alist of LaTeX macros to be passed to org-roam-ui.
+(defcustom org-gnosis-ui-latex-macros nil
+  "Alist of LaTeX macros to be passed to org-gnosis-ui.
 Format as, i.e. with double backslashes for a single backslash:
 '((\"\\macro\".\"\\something{#1}\"))"
-  :group 'org-roam-ui
+  :group 'org-gnosis-ui
   :type 'alist)
 
 ;; Internal vars
 
-(defvar org-roam-ui-root-dir
+(defvar org-gnosis-ui-root-dir
   (concat (file-name-directory
            (expand-file-name (or
                     load-file-name
                     buffer-file-name)))
           ".")
-  "Root directory of the org-roam-ui project.")
+  "Root directory of the org-gnosis-ui project.")
 
-(defvar org-roam-ui-app-build-dir
-  (expand-file-name "./out/" org-roam-ui-root-dir)
-  "Directory containing org-roam-ui's web build.")
+(defvar org-gnosis-ui-app-build-dir
+  (expand-file-name "./out/" org-gnosis-ui-root-dir)
+  "Directory containing org-gnosis-ui's web build.")
 
-(defvar org-roam-ui--ws-current-node nil
+(defvar org-gnosis-ui--ws-current-node nil
   "Var to keep track of which node you are looking at.")
 
-(defvar org-roam-ui-ws-socket nil
-  "The websocket for org-roam-ui.")
+(defvar org-gnosis-ui-ws-socket nil
+  "The websocket for org-gnosis-ui.")
 
-(defvar org-roam-ui--window nil
+(defvar org-gnosis-ui--window nil
   "The window for displaying nodes opened from within ORUI.
 This is mostly to prevent issues with EXWM and the Webkit browser.")
 
-(defvar org-roam-ui-ws-server nil
-  "The websocket server for org-roam-ui.")
+(defvar org-gnosis-ui-ws-server nil
+  "The websocket server for org-gnosis-ui.")
 
 ;;;###autoload
 (define-minor-mode
-  org-roam-ui-mode
-  "Enable org-roam-ui.
+  org-gnosis-ui-mode
+  "Enable org-gnosis-ui.
 This serves the web-build and API over HTTP."
-  :lighter " org-roam-ui"
+  :lighter " org-gnosis-ui"
   :global t
-  :group 'org-roam-ui
+  :group 'org-gnosis-ui
   :init-value nil
   (cond
-   (org-roam-ui-mode
+   (org-gnosis-ui-mode
    ;;; check if the default keywords actually exist on `orb-preformat-keywords'
    ;;; else add them
-    (setq-local httpd-port org-roam-ui-port)
-    (setq httpd-root org-roam-ui-app-build-dir)
+    (setq-local httpd-port org-gnosis-ui-port)
+    (setq httpd-root org-gnosis-ui-app-build-dir)
     (httpd-start)
-    (setq org-roam-ui-ws-server
+    (setq org-gnosis-ui-ws-server
           (websocket-server
            35903
            :host 'local
-           :on-open #'org-roam-ui--ws-on-open
-           :on-message #'org-roam-ui--ws-on-message
-           :on-close #'org-roam-ui--ws-on-close))
-    (when org-roam-ui-open-on-start (org-roam-ui-open)))
+           :on-open #'org-gnosis-ui--ws-on-open
+           :on-message #'org-gnosis-ui--ws-on-message
+           :on-close #'org-gnosis-ui--ws-on-close))
+    (when org-gnosis-ui-open-on-start (org-gnosis-ui-open)))
    (t
     (progn
-      (websocket-server-close org-roam-ui-ws-server)
+      (websocket-server-close org-gnosis-ui-ws-server)
       (httpd-stop)
-      (remove-hook 'after-save-hook #'org-roam-ui--on-save)
-      (org-roam-ui-follow-mode -1)))))
+      (remove-hook 'after-save-hook #'org-gnosis-ui--on-save)
+      (org-gnosis-ui-follow-mode -1)))))
 
-(defun org-roam-ui--log-data (message data)
+(defun org-gnosis-ui--log-data (message data)
   "Log MESSAGE along with DATA for debugging purposes."
   (message "%s: %s" message (if (stringp data) data (prin1-to-string data))))
 
-(defun org-roam-ui--ws-on-open (ws)
-  "Open the websocket WS to org-roam-ui and send initial data."
+(defun org-gnosis-ui--ws-on-open (ws)
+  "Open the websocket WS to org-gnosis-ui and send initial data."
   (when (websocket-openp ws)
-    (setq org-roam-ui-ws-socket ws)
-    (org-roam-ui--log-data "WebSocket opened." nil)
+    (setq org-gnosis-ui-ws-socket ws)
+    (org-gnosis-ui--log-data "WebSocket opened." nil)
     (condition-case err
         (progn
-          (org-roam-ui--send-variables ws)
-          (org-roam-ui--send-graphdata))
+          (org-gnosis-ui--send-variables ws)
+          (org-gnosis-ui--send-graphdata))
       (error (message "Error while sending data on open: %S" err)))
-    (when org-roam-ui-update-on-save
-      (add-hook 'after-save-hook #'org-roam-ui--on-save))
-    (when org-roam-ui-follow
-      (org-roam-ui-follow-mode 1))
-    (message "Connection established with org-roam-ui.")))
-
-(defun org-roam-ui--ws-on-message (_ws frame)
-  "Functions to run when the org-roam-ui server receives a message.
+    (when org-gnosis-ui-update-on-save
+      (add-hook 'after-save-hook #'org-gnosis-ui--on-save))
+    (when org-gnosis-ui-follow
+      (org-gnosis-ui-follow-mode 1))
+    (message "Connection established with org-gnosis-ui.")))
+
+(defun org-gnosis-ui--ws-on-message (_ws frame)
+  "Functions to run when the org-gnosis-ui server receives a message.
 Takes _WS and FRAME as arguments."
   (let* ((msg (json-parse-string
                (websocket-frame-text frame) :object-type 'alist))
          (command (alist-get 'command msg))
          (data (alist-get 'data msg)))
     (cond ((string= command "open")
-           (org-roam-ui--on-msg-open-node data))
+           (org-gnosis-ui--on-msg-open-node data))
           ((string= command "delete")
-           (org-roam-ui--on-msg-delete-node data))
+           (org-gnosis-ui--on-msg-delete-node data))
           ((string= command "create")
-           (org-roam-ui--on-msg-create-node data))
+           (org-gnosis-ui--on-msg-create-node data))
           (t
            (message
-            "Something went wrong when receiving a message from org-roam-ui")))))
+            "Something went wrong when receiving a message from org-gnosis-ui")))))
 
-(defun org-roam-ui--on-msg-open-node (data)
+(defun org-gnosis-ui--on-msg-open-node (data)
   "Open a node when receiving DATA from the websocket."
   (let* ((id (alist-get 'id data))
           (node (org-roam-node-from-id id))
           (pos (org-roam-node-point node))
           (buf (find-file-noselect (org-roam-node-file node))))
-    (run-hook-with-args 'org-roam-ui-before-open-node-functions id)
-    (unless (window-live-p org-roam-ui--window)
+    (run-hook-with-args 'org-gnosis-ui-before-open-node-functions id)
+    (unless (window-live-p org-gnosis-ui--window)
       (if-let ((windows (window-list))
                (or-windows (seq-filter
                             (lambda (window)
-                              (org-roam-buffer-p
-                               (window-buffer window))) windows))
+                              (when (bound-and-true-p org-gnosis-mode)
+				(window-buffer window)))
+			    windows))
                (newest-window (car
                                (seq-sort-by
                                 #'window-use-time #'> or-windows))))
-          (setq org-roam-ui--window newest-window)
+          (setq org-gnosis-ui--window newest-window)
         (split-window-horizontally)
-        (setq org-roam-ui--window (frame-selected-window))))
-    (set-window-buffer org-roam-ui--window buf)
-    (select-window org-roam-ui--window)
+        (setq org-gnosis-ui--window (frame-selected-window))))
+    (set-window-buffer org-gnosis-ui--window buf)
+    (select-window org-gnosis-ui--window)
     (goto-char pos)
-    (run-hook-with-args 'org-roam-ui-after-open-node-functions id)))
+    (run-hook-with-args 'org-gnosis-ui-after-open-node-functions id)))
 
-(defun org-roam-ui--on-msg-delete-node (data)
+(defun org-gnosis-ui--on-msg-delete-node (data)
   "Delete a node when receiving DATA from the websocket.
 
 TODO: Be able to delete individual nodes."
@@ -295,9 +307,9 @@ TODO: Be able to delete individual nodes."
     (message "Deleted %s" (alist-get 'file data))
     (delete-file (alist-get 'file data))
     (org-roam-db-sync)
-    (org-roam-ui--send-graphdata)))
+    (org-gnosis-ui--send-graphdata)))
 
-(defun org-roam-ui--on-msg-create-node (data)
+(defun org-gnosis-ui--on-msg-create-node (data)
   "Create a node when receiving DATA from the websocket."
   (progn
     (if (and (fboundp #'orb-edit-note) (alist-get 'ROAM_REFS data))
@@ -306,13 +318,13 @@ TODO: Be able to delete individual nodes."
      :node (org-roam-node-create :title (alist-get 'title data))
      :props '(:finalize find-file))))
 
-(defun org-roam-ui--ws-on-close (_websocket)
-  "What to do when _WEBSOCKET to org-roam-ui is closed."
-  (remove-hook 'after-save-hook #'org-roam-ui--on-save)
-  (org-roam-ui-follow-mode -1)
-  (message "Connection with org-roam-ui closed."))
+(defun org-gnosis-ui--ws-on-close (_websocket)
+  "What to do when _WEBSOCKET to org-gnosis-ui is closed."
+  (remove-hook 'after-save-hook #'org-gnosis-ui--on-save)
+  (org-gnosis-ui-follow-mode -1)
+  (message "Connection with org-gnosis-ui closed."))
 
-(defun org-roam-ui--get-text (id)
+(defun org-gnosis-ui--get-text (id)
   "Retrieve the text from org-node ID."
   (let*
       ((node (org-roam-populate (org-roam-node-create
@@ -326,9 +338,9 @@ TODO: Be able to delete individual nodes."
         (org-narrow-to-element))
       (buffer-substring-no-properties (buffer-end -1) (buffer-end 1)))))
 
-(defun org-roam-ui--send-text (id ws)
+(defun org-gnosis-ui--send-text (id ws)
   "Send the text from org-node ID through the websocket WS."
-  (let ((text (org-roam-ui--get-text id)))
+  (let ((text (org-gnosis-ui--get-text id)))
     (websocket-send-text ws
                          (json-encode
                           `((type . "orgText")
@@ -336,7 +348,7 @@ TODO: Be able to delete individual nodes."
 
 (defservlet* node/:id text/plain ()
   "Servlet for accessing node content."
-  (insert (org-roam-ui--get-text (org-link-decode id)))
+  (insert (org-gnosis-ui--get-text (org-link-decode id)))
   (httpd-send-header t "text/plain" 200 :Access-Control-Allow-Origin "*"))
 
 (defservlet* img/:file text/plain ()
@@ -345,28 +357,28 @@ TODO: Be able to delete individual nodes."
     (httpd-send-file t (org-link-decode file))
     (httpd-send-header t "text/plain" 200 :Access-Control-Allow-Origin "*")))
 
-(defun org-roam-ui--on-save ()
+(defun org-gnosis-ui--on-save ()
   "Send graphdata on saving an org-roam buffer.
 
 TODO: Make this only send the changes to the graph data, not the complete graph."
   (when (bound-and-true-p org-gnosis-mode)
-    (org-roam-ui--send-variables org-roam-ui-ws-socket)
-    (org-roam-ui--send-graphdata)))
+    (org-gnosis-ui--send-variables org-gnosis-ui-ws-socket)
+    (org-gnosis-ui--send-graphdata)))
 
-(defun org-roam-ui--check-orb-keywords ()
+(defun org-gnosis-ui--check-orb-keywords ()
   "Check if the default keywords are in `orb-preformat-keywords', if not, add them."
-  (when (and org-roam-ui-retitle-ref-nodes (boundp 'orb-preformat-keywords))
+  (when (and org-gnosis-ui-retitle-ref-nodes (boundp 'orb-preformat-keywords))
     (dolist (keyword '("author-abbrev" "year" "title"))
       (unless (seq-contains-p orb-preformat-keywords keyword)
         (setq orb-preformat-keywords
               (append orb-preformat-keywords (list keyword)))))))
 
-(defun org-roam-ui--find-ref-title (ref)
+(defun org-gnosis-ui--find-ref-title (ref)
   "Find the title of the bibtex entry keyed by `REF'.
 
 Requires `org-roam-bibtex' and `bibtex-completion' (a dependency of `orb') to be
 loaded. Returns `ref' if an entry could not be found."
-  (if (and org-roam-ui-find-ref-title
+  (if (and org-gnosis-ui-find-ref-title
            (fboundp 'bibtex-completion-get-entry)
            (fboundp 'orb--pre-expand-template)
            (boundp 'orb-preformat-keywords))
@@ -378,17 +390,17 @@ loaded. Returns `ref' if an entry could not be found."
           ;; matters. Interpolate the bibtex entries, and extract the filled
           ;; template from the return value.
           (nth 3 (orb--pre-expand-template
-                  `("" "" plain ,org-roam-ui-ref-title-template) entry))
+                  `("" "" plain ,org-gnosis-ui-ref-title-template) entry))
         ref)
     ref))
 
-(defun org-roam-ui--replace-nth (el n lst)
+(defun org-gnosis-ui--replace-nth (el n lst)
   "Non-destructively replace the `N'th element of `LST' with `EL'."
   (let ((head (butlast lst (- (length lst) n)))
         (tail (nthcdr (+ n 1) lst)))
     (append head (list el) tail)))
 
-(defun org-roam-ui--citekey-to-ref (citekey)
+(defun org-gnosis-ui--citekey-to-ref (citekey)
   "Convert a CITEKEY property (most likely with a `cite:' prefix) to just a key.
 
 This method is mostly taken from `org-roam-bibtex'
@@ -403,32 +415,32 @@ the `org-ref-cite-re'"
           (when (string-match org-ref-cite-re c)
             (throw 'found (match-string 2 c)))))))
 
-(defun org-roam-ui--retitle-node (node)
+(defun org-gnosis-ui--retitle-node (node)
   "Replace the title of citation NODE with associated notes.
 
 A new title is created using information from the bibliography and formatted
-according to `org-roam-ui-ref-title-template', just like the citation nodes with
+according to `org-gnosis-ui-ref-title-template', just like the citation nodes with
 a note are. It requires `org-roam-bibtex' and it's dependencies
 \(`bibtex-completion' and `org-ref'\) to be loaded.
 
 Returns the node with an updated title if the current node is a reference node
 and the key was found in the bibliography, otherwise the node is returned
 unchanged."
-  (if-let* (org-roam-ui-retitle-ref-nodes
+  (if-let* (org-gnosis-ui-retitle-ref-nodes
             ;; set a fake var because if-let(((boundp 'fake-var))) returns true
             (orcr (boundp 'org-ref-cite-re))
             (citekey (cdr (assoc "ROAM_REFS" (nth 5 node))))
-            (ref (org-roam-ui--citekey-to-ref citekey))
-            (title (org-roam-ui--find-ref-title ref)))
-      (org-roam-ui--replace-nth title 2 node)
+            (ref (org-gnosis-ui--citekey-to-ref citekey))
+            (title (org-gnosis-ui--find-ref-title ref)))
+      (org-gnosis-ui--replace-nth title 2 node)
     node))
 
-(defun org-roam-ui--create-fake-node (ref)
+(defun org-gnosis-ui--create-fake-node (ref)
   "Create a fake node for REF without a source note."
   (list
    ref
    ref
-   (org-roam-ui--find-ref-title ref)
+   (org-gnosis-ui--find-ref-title ref)
    0
    0
    'nil
@@ -436,87 +448,62 @@ unchanged."
      ("FILELESS" . t))
    'nil))
 
-(defun org-roam-ui-get-links (&optional old-db)
-  "Fetch links from the org-roam database.
-If OLD-DB is non-nil, use the older method of getting links."
-  (if old-db
-      (org-roam-ui--separate-ref-links
-       (org-roam-ui--get-links t))
-    (nconc (org-roam-ui--separate-ref-links
-            (org-roam-ui--get-cites))
-           (org-roam-ui--get-links))))
-
-(defun org-roam-ui-get-tags ()
+(defun org-gnosis-ui-get-tags ()
   "Fetch tags from the org-roam database."
   (seq-mapcat #'seq-reverse
               (org-roam-db-query
                [:select :distinct tag :from tags])))
 
-(defun org-roam-ui-get-nodes (&optional nodes links-db)
+(defun org-gnosis-ui-get-nodes (&optional nodes links-db)
   "Fetch nodes and create fake nodes based on LINKS-DB.
 If NODES is provided, use it directly."
-  (let* ((nodes-db (or nodes (org-roam-ui--get-nodes)))
-         (fake-nodes (seq-map #'org-roam-ui--create-fake-node
+  (let* ((nodes-db (or nodes (org-gnosis-ui--get-nodes)))
+         (fake-nodes (seq-map #'org-gnosis-ui--create-fake-node
                               (delete-dups
                                (mapcar #'cadr
-                                       (org-roam-ui--filter-citations links-db))))))
-    (append (if org-roam-ui-retitle-ref-nodes
-                (seq-map #'org-roam-ui--retitle-node nodes-db)
+                                       (org-gnosis-ui--filter-citations links-db))))))
+    (append (if org-gnosis-ui-retitle-ref-nodes
+                (seq-map #'org-gnosis-ui--retitle-node nodes-db)
               nodes-db)
             fake-nodes)))
 
-(defun org-roam-ui--send-graphdata (&optional nodes links tags)
-  "Prepare and send graph data to org-roam-ui, optionally using NODES, LINKS, and TAGS.
+(defun org-gnosis-ui--send-graphdata (&optional nodes links tags)
+  "Prepare and send graph data to org-gnosis-ui, optionally using NODES, LINKS, and TAGS.
 If not provided, data is retrieved from the org-roam database."
-  (let* ((links-db (or links (funcall org-roam-ui-links-function)))
-         (nodes-db (or nodes (funcall org-roam-ui-nodes-function)))
-         (tags-db (or tags (funcall org-roam-ui-tags-function)))
+  (let* ((links-db (or links (funcall org-gnosis-ui-links-function)))
+         (nodes-db (or nodes (funcall org-gnosis-ui-nodes-function)))
+         (tags-db (or tags (funcall org-gnosis-ui-tags-function)))
          (nodes-alist '())
          (links-alist '()))
     
     ;; Convert nodes to alist
     (dolist (node nodes-db)
-      (push (org-roam-ui-sql-to-alist
+      (push (org-gnosis-ui-sql-to-alist
              '(id file title level pos olp properties tags) node)
             nodes-alist))
     
     ;; Convert links to alist
     (dolist (link links-db)
-      (push (org-roam-ui-sql-to-alist
+      (push (org-gnosis-ui-sql-to-alist
              '(source target type) link)
             links-alist))
     
     (let ((response `((nodes . ,nodes-alist)
                       (links . ,links-alist)
                       (tags . ,tags-db))))
-      (websocket-send-text org-roam-ui-ws-socket
+      (websocket-send-text org-gnosis-ui-ws-socket
                            (json-encode `((type . "graphdata") (data . ,response)))))))
 
 
-(defun org-roam-ui--filter-citations (links)
+(defun org-gnosis-ui--filter-citations (links)
   "Filter out the citations from LINKS."
   (seq-filter
    (lambda (link)
      (string-match-p "cite" (nth 2 link)))
    links))
-;;;; Databse query for org-roam
-;; (defun org-roam-ui-query ()
-;;   "Database query."
-;;   (org-roam-db-query
-;;    [:select [id
-;;              file
-;;              title
-;;              level
-;;              (funcall group-concat tag
-;;                       (emacsql-escape-raw \, ))]
-;;             :as tags
-;;             :from nodes
-;;             :left-join tags
-;;             :on (= id node_id)
-;;             :group :by id]))
 
 ;; Query for gnosis
-(defun org-roam-ui-query ()
+(defun org-gnosis-ui-query ()
   "Query to get nodes from org-gnosis db."
   (emacsql org-gnosis-db
 	   [:select [id file title level
@@ -528,8 +515,8 @@ If not provided, data is retrieved from the org-roam database."
 		    :on (= id id)
 		    :group :by id]))
 
-(defun org-roam-ui--get-nodes ()
-  "Fetch nodes to display in org-roam-ui with properly structured output."
+(defun org-gnosis-ui--get-nodes ()
+  "Fetch nodes to display in org-gnosis-ui with properly structured output."
   (mapcar (lambda (node)
             (let ((id (nth 0 node))
                   (file (nth 1 node))
@@ -551,88 +538,25 @@ If not provided, data is retrieved from the org-roam database."
                           (cons "FILE" file)
                           (cons "PRIORITY" "B"))
                     tags))) ;; Put tags at the last position as per your requirement
-          (org-roam-ui-query)))
-
-(defun org-roam-ui--get-links (&optional old)
-  "Get the cites and links tables as rows from the org-roam db.
-Optionally set OLD to t to use the old db model (where the cites
-were in the same table as the links)."
-(if (not old)
-    (org-roam-db-query
-     `[:select  [links:source
-                 links:dest
-                 links:type]
-       :from links
-       :where (= links:type "id")])
-  ;; Left outer join on refs means any id link (or cite link without a
-  ;; corresponding node) will have 'nil for the `refs:node-id' value. Any
-  ;; cite link where a node has that `:ROAM_REFS:' will have a value.
-  (org-roam-db-query
-   `[:select [links:source
-              links:dest
-              links:type
-              refs:node-id]
-     :from links
-     :left :outer :join refs :on (= links:dest refs:ref)
-     :where (or
-             (= links:type "id")
-             (like links:type "%cite%"))])))
-
-(defun org-roam-ui--get-cites ()
-  "Get the citations when using the new db-model."
-  (org-roam-db-query
-   `[:select [citations:node-id citations:cite-key refs:node-id]
-     :from citations
-     :left :outer :join refs :on (= citations:cite-key refs:ref)]))
-
-(defun org-roam-ui--separate-ref-links (links &optional old)
-  "Create separate entries for LINKS with existing reference nodes.
-Optionally set OLD to t to support old citations db-model.
-
-Convert any cite links that have nodes with associated refs to an
-id based link of type `ref' while removing the 'nil `refs:node-id'
-from all other links."
-
- (if (not old)
-    (seq-map
-     (lambda (link)
-       (pcase-let ((`(,source ,dest ,node-id) link))
-         (if node-id
-             (list source node-id "ref")
-           (list source dest "cite"))))
-     links)
-   (seq-map
-    (lambda (link)
-      (pcase-let ((`(,source ,dest ,type ,node-id) link))
-        (if node-id
-            (list source node-id "ref")
-          (list source dest type))))
-    links)))
-
-(defun org-roam-ui--update-current-node ()
+          (funcall org-gnosis-ui-node-query)))
+
+(defun org-gnosis-ui--update-current-node ()
   "Send the current node data to the web-socket."
-  (when (and (websocket-openp org-roam-ui-ws-socket)
+  (when (and (websocket-openp org-gnosis-ui-ws-socket)
              (bound-and-true-p org-gnosis-mode)
              (buffer-file-name (buffer-base-buffer)))
     (let* ((node (org-gnosis-get-id)))
-      (setq org-roam-ui--ws-current-node node)
-      (websocket-send-text org-roam-ui-ws-socket
+      (setq org-gnosis-ui--ws-current-node node)
+      (websocket-send-text org-gnosis-ui-ws-socket
                            (json-encode `((type . "command")
                                           (data . ((commandName . "follow")
-                                                   (id . ,node))))))
-      ;; (unless (string= org-roam-ui--ws-current-node node)
-      ;;   (setq org-roam-ui--ws-current-node node)
-      ;;   (websocket-send-text org-roam-ui-ws-socket
-      ;;                        (json-encode `((type . "command")
-      ;;                                       (data . ((commandName . "follow")
-      ;;                                                (id . ,node)))))))
-      )))
+                                                   (id . ,node)))))))))
 
 
-(defun org-roam-ui--update-theme ()
+(defun org-gnosis-ui--update-theme ()
   "Send the current theme data to the websocket."
   (let  ((ui-theme (list nil)))
-    (if org-roam-ui-sync-theme
+    (if org-gnosis-ui-sync-theme
         (if (boundp 'doom-themes--colors)
             (let*
                 ((colors (butlast doom-themes--colors
@@ -644,28 +568,28 @@ from all other links."
                    (cons (car color) (car (cdr color)))
                    doom-theme)))
               (setq ui-theme doom-theme))
-          (setq ui-theme (org-roam-ui-get-theme)))
-      (when org-roam-ui-custom-theme
-		(setq ui-theme org-roam-ui-custom-theme)))
+          (setq ui-theme (org-gnosis-ui-get-theme)))
+      (when org-gnosis-ui-custom-theme
+		(setq ui-theme org-gnosis-ui-custom-theme)))
     ui-theme))
 
 
-(defun org-roam-ui--send-variables (ws)
+(defun org-gnosis-ui--send-variables (ws)
   "Send miscellaneous org-roam variables through the websocket WS."
-  (let ((daily-dir (or org-roam-ui-dailies-directory ""))
+  (let ((daily-dir (or org-gnosis-ui-dailies-directory ""))
         (attach-dir (or (and (boundp 'org-attach-id-dir) org-attach-id-dir)
                         (expand-file-name ".attach/" org-directory)))
         (use-inheritance (or (and (boundp 'org-attach-use-inheritance)
                                   org-attach-use-inheritance)
                              nil))
-        (sub-dirs (or (org-roam-ui-find-subdirectories) (list ""))))
-    (org-roam-ui--log-data "Sending variables"
+        (sub-dirs (or (org-gnosis-ui-find-subdirectories) (list ""))))
+    (org-gnosis-ui--log-data "Sending variables"
                            `(("subDirs" . ,sub-dirs)
                              ("dailyDir" . ,daily-dir)
                              ("attachDir" . ,attach-dir)
                              ("useInheritance" . ,use-inheritance)
-                             ("roamDir" . ,(or org-roam-ui-directory ""))
-                             ("katexMacros" . ,(or org-roam-ui-latex-macros '()))))
+                             ("roamDir" . ,(or org-gnosis-ui-directory ""))
+                             ("katexMacros" . ,(or org-gnosis-ui-latex-macros '()))))
     (websocket-send-text ws
                          (json-encode
                           `((type . "variables")
@@ -674,10 +598,10 @@ from all other links."
                                    ("dailyDir" . ,daily-dir)
                                    ("attachDir" . ,attach-dir)
                                    ("useInheritance" . ,use-inheritance)
-                                   ("roamDir" . ,(or org-roam-ui-directory ""))
-                                   ("katexMacros" . ,(or org-roam-ui-latex-macros '())))))))))
+                                   ("roamDir" . ,(or org-gnosis-ui-directory ""))
+                                   ("katexMacros" . ,(or org-gnosis-ui-latex-macros '())))))))))
 
-(defun org-roam-ui-sql-to-alist (column-names rows)
+(defun org-gnosis-ui-sql-to-alist (column-names rows)
   "Convert sql result to alist for json encoding.
 ROWS is the sql result, while COLUMN-names is the columns to use."
   (let (res)
@@ -696,7 +620,7 @@ ROWS is the sql result, while COLUMN-names is the columns to use."
         (setq rows nil))))
     res))
 
-(defun org-roam-ui-get-theme ()
+(defun org-gnosis-ui-get-theme ()
   "Attempt to bring the current theme into a standardized format."
   (list `(bg . ,(face-background hl-line-face))
         `(bg-alt . ,(face-background 'default))
@@ -711,15 +635,15 @@ ROWS is the sql result, while COLUMN-names is the columns to use."
         `(violet . ,(face-foreground font-lock-constant-face))
         `(magenta . ,(face-foreground font-lock-preprocessor-face))))
 
-(defun org-roam-ui-find-subdirectories ()
+(defun org-gnosis-ui-find-subdirectories ()
   "Find all the subdirectories in the org-roam directory.
 TODO: Exclude org-attach dirs."
    (seq-filter
-    (lambda (file) (and (file-directory-p file) (org-roam-ui-allowed-directory-p file)))
-    (directory-files-recursively org-roam-ui-directory
-                                 ".*" t #'org-roam-ui-allowed-directory-p)))
+    (lambda (file) (and (file-directory-p file) (org-gnosis-ui-allowed-directory-p file)))
+    (directory-files-recursively org-gnosis-ui-directory
+                                 ".*" t #'org-gnosis-ui-allowed-directory-p)))
 
-(defun org-roam-ui-allowed-directory-p (dir)
+(defun org-gnosis-ui-allowed-directory-p (dir)
   "Check whether a DIR should be listed as a filterable dir.
 Hides . directories."
   (not (string-match-p "\\(\/\\|\\\\\\)\\..*?"  dir)))
@@ -727,15 +651,15 @@ Hides . directories."
 ;;;; interactive commands
 
 ;;;###autoload
-(defun org-roam-ui-open ()
-  "Ensure `org-roam-ui' is running, then open the `org-roam-ui' webpage."
+(defun org-gnosis-ui-open ()
+  "Ensure `org-gnosis-ui' is running, then open the `org-gnosis-ui' webpage."
   (interactive)
-  (unless org-roam-ui-mode (org-roam-ui-mode))
-  (funcall org-roam-ui-browser-function
-           (format "http://localhost:%d" org-roam-ui-port)))
+  (unless org-gnosis-ui-mode (org-gnosis-ui-mode))
+  (funcall org-gnosis-ui-browser-function
+           (format "http://localhost:%d" org-gnosis-ui-port)))
 
 ;;;###autoload
-(defun org-roam-ui-node-zoom (&optional id speed padding)
+(defun org-gnosis-ui-node-zoom (&optional id speed padding)
   "Move the view of the graph to current node.
 or optionally a node of your choosing.
 Optionally takes three arguments:
@@ -744,7 +668,7 @@ The SPEED in ms it takes to make the transition.
 The PADDING around the nodes in the viewport."
   (interactive)
   (if-let ((node (or id (org-gnosis-get-id))))
-      (websocket-send-text org-roam-ui-ws-socket
+      (websocket-send-text org-gnosis-ui-ws-socket
                            (json-encode `((type . "command")
                                           (data . ((commandName . "zoom")
                                                    (id . ,node)
@@ -754,12 +678,12 @@ The PADDING around the nodes in the viewport."
 
 
 ;;;###autoload
-(defun org-roam-ui-node-local (&optional id speed padding)
+(defun org-gnosis-ui-node-local (&optional id speed padding)
   "Open the local graph view of the current node.
 Optionally with ID (string), SPEED (number, ms) and PADDING (number, px)."
   (interactive)
   (if-let ((node (or id (org-gnosis-get-id))))
-      (websocket-send-text org-roam-ui-ws-socket
+      (websocket-send-text org-gnosis-ui-ws-socket
                            (json-encode `((type . "command")
                                           (data . ((commandName . "local")
                                                    (id . ,node)
@@ -768,11 +692,11 @@ Optionally with ID (string), SPEED (number, ms) and PADDING (number, px)."
     (message "No node found.")))
 
 
-(defun org-roam-ui-change-local-graph (&optional id manipulation)
+(defun org-gnosis-ui-change-local-graph (&optional id manipulation)
   "Add or remove current node to the local graph. If not in local mode, open local-graph for this node."  
   (interactive)
   (if-let ((node (or id (org-gnosis-get-id))))
-      (websocket-send-text org-roam-ui-ws-socket
+      (websocket-send-text org-gnosis-ui-ws-socket
                            (json-encode `((type . "command")
                                           (data . ((commandName . "change-local-graph")
                                                    (id . ,node)
@@ -780,44 +704,44 @@ Optionally with ID (string), SPEED (number, ms) and PADDING (number, px)."
     (message "No node found.")))
 
 ;;;###autoload
-(defun org-roam-ui-add-to-local-graph (&optional id)
+(defun org-gnosis-ui-add-to-local-graph (&optional id)
   "Add current node to the local graph. If not in local mode, open local-graph for this node."
   (interactive)
-  (org-roam-ui-change-local-graph id "add"))
+  (org-gnosis-ui-change-local-graph id "add"))
 
 ;;;###autoload
-(defun org-roam-ui-remove-from-local-graph (&optional id)
+(defun org-gnosis-ui-remove-from-local-graph (&optional id)
   "Remove current node from the local graph. If not in local mode, open local-graph for this node."
   (interactive)
-  (org-roam-ui-change-local-graph id "remove"))
+  (org-gnosis-ui-change-local-graph id "remove"))
 
 ;;;###autoload
-(defun org-roam-ui-sync-theme ()
-  "Sync your current Emacs theme with org-roam-ui."
+(defun org-gnosis-ui-sync-theme ()
+  "Sync your current Emacs theme with org-gnosis-ui."
   (interactive)
-  (websocket-send-text org-roam-ui-ws-socket
+  (websocket-send-text org-gnosis-ui-ws-socket
                        (json-encode `((type . "theme")
-                                      (data . ,(org-roam-ui--update-theme))))))
+                                      (data . ,(org-gnosis-ui--update-theme))))))
 
 ;;; Obsolete commands
-(define-obsolete-function-alias #'orui-open #'org-roam-ui-open "0.1")
-(define-obsolete-function-alias #'orui-node-local #'org-roam-ui-node-local "0.1")
-(define-obsolete-function-alias #'orui-node-zoom #'org-roam-ui-node-zoom "0.1")
-(define-obsolete-function-alias #'orui-sync-theme #'org-roam-ui-sync-theme "0.1")
+(define-obsolete-function-alias #'orui-open #'org-gnosis-ui-open "0.1")
+(define-obsolete-function-alias #'orui-node-local #'org-gnosis-ui-node-local "0.1")
+(define-obsolete-function-alias #'orui-node-zoom #'org-gnosis-ui-node-zoom "0.1")
+(define-obsolete-function-alias #'orui-sync-theme #'org-gnosis-ui-sync-theme "0.1")
 
 ;;;###autoload
-(define-minor-mode org-roam-ui-follow-mode
+(define-minor-mode org-gnosis-ui-follow-mode
   "Set whether ORUI should follow your every move in Emacs."
-  :lighter " org-roam-ui"
+  :lighter " org-gnosis-ui"
   :global t
-  :group 'org-roam-ui
+  :group 'org-gnosis-ui
   :init-value nil
-  (if org-roam-ui-follow-mode
+  (if org-gnosis-ui-follow-mode
       (progn
-        (add-hook 'post-command-hook #'org-roam-ui--update-current-node)
-        (message "org-roam-ui will now follow you around."))
-    (remove-hook 'post-command-hook #'org-roam-ui--update-current-node)
-    (message "org-roam-ui will now leave you alone.")))
+        (add-hook 'post-command-hook #'org-gnosis-ui--update-current-node)
+        (message "org-gnosis-ui will now follow you around."))
+    (remove-hook 'post-command-hook #'org-gnosis-ui--update-current-node)
+    (message "org-gnosis-ui will now leave you alone.")))
 
-(provide 'org-roam-ui)
-;;; org-roam-ui.el ends here
+(provide 'org-gnosis-ui)
+;;; org-gnosis-ui.el ends here