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;;; org-gnosis.el --- Org Note Management System -*- lexical-binding: t; -*-
;; Copyright (C) 2024-2025 Thanos Apollo
;; Author: Thanos Apollo <[email protected]>
;; Keywords: extensions
;; URL: https://thanosapollo.org/projects/gnosis
;; Version: 0.0.1
;; Package-Requires: ((emacs "27.2") (emacsql "4.0.3") (compat "29.1.4.2"))
;; 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 <https://www.gnu.org/licenses/>.
;;; Commentary:
;; Under development
;;; Code:
(require 'cl-lib)
(require 'emacsql-sqlite)
(require 'org-element)
(defgroup org-gnosis nil
"Note Taking System."
:group 'external)
(defcustom org-gnosis-dir "~/Notes"
"Directory with gnosis notes."
:type 'directory
:group 'org-gnosis)
(defcustom org-gnosis-journal-template
"* Daily Notes\n\n* Goals\n+ []"
"Template for journaling."
:type 'string
:group 'org-gnosis)
(defcustom org-gnosis-journal-dir (expand-file-name "journal" org-gnosis-dir)
"Gnosis journal directory."
:type 'directory
:group 'org-gnosis)
(defcustom org-gnosis-show-tags nil
"Display tags with `org-gnosis-find'."
:type 'boolean
:group 'org-gnosis)
(defface org-gnosis-face-tags
'((t :inherit font-lock-type-face))
"Face for displaying gnosis with `org-gnosis-find'."
:group 'org-gnosis)
(defvar org-gnosis-db (emacsql-sqlite-open (locate-user-emacs-file "org-gnosis.db")))
(cl-defun org-gnosis-select (value table &optional (restrictions '1=1) (flatten nil))
"Select VALUE from TABLE, optionally with RESTRICTIONS.
Optional argument FLATTEN, when non-nil, flattens the result."
(let ((output (emacsql org-gnosis-db `[:select ,value :from ,table :where ,restrictions])))
(if flatten
(apply #'append output)
output)))
(cl-defun org-gnosis--insert-into (table values)
"Insert VALUES to TABLE."
(emacsql org-gnosis-db `[:insert :into ,table :values ,values]))
(defun org-gnosis--delete (table value)
"From TABLE use where to delete VALUE."
(emacsql org-gnosis-db `[:delete :from ,table :where ,value]))
(cl-defun org-gnosis--drop-table (table)
"Drop TABLE from `gnosis-db'."
(emacsql org-gnosis-db `[:drop-table ,table]))
(defun org-gnosis-get-current-node-title ()
"Return the title of the current node."
(when (derived-mode-p 'org-mode)
(let* ((parsed-data (org-element-parse-buffer))
(title (org-element-map parsed-data 'keyword
(lambda (kw)
(when (string-equal (org-element-property :key kw) "TITLE")
(org-element-property :value kw)))
nil t)))
title)))
(defun org-gnosis-get-filetags (&optional parsed-data)
"Return the filetags of the buffer's PARSED-DATA as a comma-separated string."
(let* ((parsed-data (or parsed-data (org-element-parse-buffer)))
(filetags (org-element-map parsed-data 'keyword
(lambda (kw)
(when (string-equal (org-element-property :key kw) "FILETAGS")
(org-element-property :value kw)))
nil t)))
(and filetags (remove "" (split-string filetags ":")))))
(defun org-gnosis-get-links (contents)
"Recursively collect all node id links from CONTENTS."
(org-element-map contents 'link
(lambda (link)
(when (string-equal "id" (org-element-property :type link))
(org-element-property :path link)))
nil nil 'headline))
(defun org-gnosis-process-node (node)
"Process a single headline NODE and return information as a list."
(let ((title (org-element-property :raw-value node))
(tags (org-element-property :tags node))
(id (org-element-property :ID node))
(links (org-gnosis-get-links (org-element-contents node)))
(children (org-element-contents node)))
(when title
(list title tags id
(org-gnosis-process-children children (1+ (org-element-property :level node)))
links))))
(defun org-gnosis-process-children (nodes level)
"Recursively process NODES at a given LEVEL."
(let (result)
(while nodes
(let ((current-node (car nodes))
(current-level (org-element-property :level (car nodes))))
(if (and current-level (= current-level level))
(progn
(push (org-gnosis-process-node current-node) result)
(setq nodes (cdr nodes)))
(setq nodes (cdr nodes)))))
(nreverse result)))
(defun org-gnosis-get-data--nodes (&optional parsed-data)
"Return a hierarchical list of nodes with titles, tags, and IDs from PARSED-DATA."
(let ((parsed-data (or parsed-data (org-element-parse-buffer))))
(org-gnosis-process-children (org-element-map parsed-data 'headline #'identity) 1)))
(defun org-gnosis-get-data--topic (&optional parsed-data)
"Retrieve the title and ID from the current org buffer or given PARSED-DATA."
(let* ((parsed-data (or parsed-data (org-element-parse-buffer)))
(title (org-element-map parsed-data 'keyword
(lambda (kw)
(when (string= (org-element-property :key kw) "TITLE")
(org-element-property :value kw)))
nil t))
(id (org-element-map parsed-data 'property-drawer
(lambda (drawer)
(org-element-map (org-element-contents drawer) 'node-property
(lambda (prop)
(when (string= (org-element-property :key prop) "ID")
(org-element-property :value prop)))
nil t))
nil t))
(tags (org-gnosis-get-filetags)))
(list title tags id)))
(defun org-gnosis-get--data (file)
"Return data for FILE.
FILE: File path"
(let* ((parsed-data (org-element-parse-buffer))
(topic (org-gnosis-get-data--topic parsed-data))
(nodes (org-gnosis-get-data--nodes parsed-data))
(filename (file-name-nondirectory file))
(links (org-gnosis-get-links parsed-data)))
`(:file ,filename :topic ,topic :nodes ,nodes :links ,links)))
(defun org-gnosis-adjust-title (input)
"Adjust the INPUT string to replace id link structures with plain text."
(when (stringp input)
(replace-regexp-in-string "\\[\\[id:[^]]+\\]\\[\\(.*?\\)\\]\\]" "\\1" input)))
(defun org-gnosis-get-file-info (filename)
"Something FILENAME."
(with-temp-buffer
(insert-file-contents filename)
(let* ((data (org-gnosis-get--data filename)))
data)))
(defun org-gnosis-parse-nodes (nodes top-node-id inherited-tags)
"Parse a list of nodes, inheriting tags and associating the top node ID.
NODES: list of nodes to parse.
TOP-NODE-ID: the ID of the top node to associate with each node.
INHERITED-TAGS: tags from the top node to inherit."
(cl-loop for (name tags id sub-nodes links) in nodes
;; Only include nodes with non-nil id
when id
append (list (list :node name
:tags (append tags inherited-tags)
:id id
:top-node top-node-id
:links links))
;; Recursively parse sub-nodes, inheriting current node's tags
append (org-gnosis-parse-nodes sub-nodes (when id id) (append tags inherited-tags))))
(defun org-gnosis-parse-data-recursive (data &optional initial-tags top-node-id)
"Recursively parse the entire data structure, extracting nodes and details.
DATA: List of top-level nodes to start parsing.
INITIAL-TAGS: Initial set of tags to inherit."
(cl-loop for (node tags id sub-nodes) in data
;; Directly parse sub-nodes, using top-level nodes only if they have valid id
append (when id (list (list :node node
:tags (append tags initial-tags)
:id id
:top-node top-node-id)))
append (org-gnosis-parse-nodes sub-nodes id (append tags initial-tags))))
(defun org-gnosis-update-file (&optional file)
"Update contents of FILE in databse.
Removes all contents of FILE in database, adding them anew."
(let* ((file (or file (file-name-nondirectory (buffer-file-name))))
(journal-p (file-in-directory-p file org-gnosis-journal-dir))
(nodes (if journal-p
(org-gnosis-select 'id 'journal `(= file ,file) t)
(org-gnosis-select 'id 'nodes `(= file ,file) t))))
(emacsql-with-transaction org-gnosis-db
;; Delete all nodes of file in db
(cl-loop for node in nodes
do (if journal-p
(org-gnosis--delete 'journal `(= id ,node))
(org-gnosis--delete 'nodes `(= id ,node))))
(if journal-p
(org-gnosis-journal--update-file file)
(org-gnosis--update-file file)))))
(defun org-gnosis--is-journal-entry-p (file)
"Check if FILE is a journal entry."
(let ((file-dir (file-name-directory (expand-file-name file)))
(expanded-dir (file-name-as-directory (expand-file-name org-gnosis-journal-dir))))
(string-equal file-dir expanded-dir)))
(defun org-gnosis--update-file (file)
"Add contents of FILE to database."
(let* ((data (org-gnosis-get-file-info file))
(file (plist-get data :file))
(topic (org-gnosis-adjust-title (nth 0 (plist-get data :topic))))
(tags (nth 1 (plist-get data :topic)))
(hash (nth 2 (plist-get data :topic))) ;; topic id
(links (plist-get data :links))) ;; main topic links
;; Add gnosis topic
(emacsql-with-transaction org-gnosis-db
(org-gnosis--insert-into 'nodes `([,hash ,file ,topic ,tags]))
(cl-loop for link in links
do (org-gnosis--insert-into 'links `([,hash ,link]))))
;; Add nodes of topic
(cl-loop for node in (org-gnosis-parse-data-recursive
(plist-get data :nodes)
tags ;; initial topic tags for top node
hash ;; node topic hash
)
do
(let ((title (org-gnosis-adjust-title (plist-get node :node)))
(tags (plist-get node :tags))
(id (plist-get node :id)))
(emacsql-with-transaction org-gnosis-db
(org-gnosis--insert-into 'nodes `([,id ,file ,title ,tags]))
;; (org-gnosis--insert-into 'links `([,id ]))
)))))
(defun org-gnosis-journal--update-file (file)
"Update database for journal FILE."
(let* ((data (org-gnosis-get-file-info file))
(file (plist-get data :file))
(tags (nth 1 (plist-get data :topic)))
(date (org-gnosis-adjust-title (nth 0 (plist-get data :topic))))
(hash (nth 2 (plist-get data :topic)))
(links (plist-get data :links)))
;; Add journal
(emacsql-with-transaction org-gnosis-db
(org-gnosis--insert-into 'journal `([,hash ,file ,date ,tags])))))
(defun org-gnosis-db-sync--journal ()
"Sync journal entries in databse."
(cl-loop for file in (cl-remove-if-not (lambda (file)
(and (string-match-p "^[0-9]"
(file-name-nondirectory file))
(not (file-directory-p file))))
(directory-files org-gnosis-journal-dir t nil t))
do (org-gnosis-journal--update-file file)))
;;;###autoload
(defun org-gnosis-db-sync (&optional arg)
"Sync `org-gnosis-db'.
If called with ARG do not initialize the database."
(interactive "P")
(unless arg
(org-gnosis-db-init))
(let ((files (cl-remove-if-not (lambda (file)
(and (string-match-p "^[0-9]" (file-name-nondirectory file))
(not (file-directory-p file))))
(directory-files org-gnosis-dir t nil t))))
(cl-loop for file in files
do (org-gnosis--update-file file)))
(org-gnosis-db-sync--journal))
(defun org-gnosis-find--tag-with-tag-prop (lst)
"Combine each sublist of strings in LST into a single string."
(mapcar (lambda (item)
(let* ((title (car item))
(tags (cadr item))
(propertized-tags
(when tags
(concat (propertize "#" 'face 'org-gnosis-face-tags)
(propertize (mapconcat 'identity tags "#")
'face 'org-gnosis-face-tags)))))
(if propertized-tags
(format "%s %s" title propertized-tags)
title)))
lst))
(defun org-gnosis--create-file (title &optional file extras)
"Create node & FILE for TITLE."
(let* ((file-name (replace-regexp-in-string "#" "" ;; hashtags are used for tags
(replace-regexp-in-string " " "-" title)))
(file (or file (expand-file-name
(format "%s--%s.org" (format-time-string "%Y%m%d%H%M%S") file-name)
org-gnosis-dir))))
(find-file file)
(unless (file-exists-p file)
(insert (format "#+title: %s\n#+filetags:\n" title))
(org-id-get-create)
(and extras (insert extras))
(org-mode)
(org-gnosis-mode)
file-name)))
(defun org-gnosis-find--with-tags (&optional prompt entries)
"Select gnosis node with tags from ENTRIES.
PROMPT: Prompt message."
(replace-regexp-in-string " #[^[:space:]]+" ""
(completing-read (or prompt "Select gnosis node: ")
(org-gnosis-find--tag-with-tag-prop
(or entries (org-gnosis-select '[title tags] 'nodes))))))
(defun org-gnosis--find (prompt entries-with-tags entries)
"PROMPT user to select from ENTRIES.
If `org-gnosis-show-tags' is non-nil, ENTRIES-WITH-TAGS will be used
instead."
(let* ((entry (if org-gnosis-show-tags
(org-gnosis-find--with-tags prompt entries-with-tags)
(completing-read prompt entries))))
entry))
;;;###autoload
(defun org-gnosis-find (&optional title file id directory)
"Select gnosis node."
(interactive)
(let* ((title (or title (if org-gnosis-show-tags
(org-gnosis-find--with-tags)
(completing-read "Select gnosis node: "
(org-gnosis-select 'title 'nodes)))))
(file (or file (caar (org-gnosis-select 'file 'nodes `(= title ,title)))))
(id (or id (caar (or id (org-gnosis-select 'id 'nodes `(= title ,title))))))
(directory (or directory org-gnosis-dir)))
(cond ((null file)
(org-gnosis--create-file title))
((file-exists-p (expand-file-name file directory))
(find-file
(expand-file-name file directory))
(ignore-errors (org-id-goto id))
(org-gnosis-mode 1)))))
;;;###autoload
(defun org-gnosis-insert ()
"Insert gnosis node."
(interactive)
(let* ((node (org-gnosis--find "Select gnosis node: "
(org-gnosis-select '[title tags] 'nodes '1=1)
(org-gnosis-select 'title 'nodes '1=1)))
(id (concat "id:" (car (org-gnosis-select 'id 'nodes `(= ,node title) '1=1)))))
(org-insert-link nil id node)))
;;;###autoload
(defun org-gnosis-journal-find (&optional date)
"Find journal entry for DATE."
(interactive)
(let* ((prompt "Select journal entry")
(date (or date (org-gnosis--find
prompt
(org-gnosis-select '[date tags] 'journal)
(org-gnosis-select 'date 'journal))))
(id (car (org-gnosis-select 'id 'journal `(= date ,date) t)))
(file (car (org-gnosis-select 'file 'journal `(= date ,date) t))))
(org-gnosis-find date file id org-gnosis-journal-dir)))
;;;###autoload
(defun org-gnosis-journal-insert ()
"Insert journal entry."
(interactive)
(let* ((node (org-gnosis--find "Select journal entry: "
(org-gnosis-select '[date tags] 'journal '1=1)
(org-gnosis-select 'date 'journal '1=1)))
(node-id (concat "id:" (car (org-gnosis-select 'id 'journal `(= ,node date) '1=1)))))
(org-insert-link nil node-id node)))
(defun org-gnosis-journal (&optional template)
"Start journaling for current date."
(interactive)
(let* ((date (format-time-string "%Y-%m-%d"))
(file (format "%s.org" date)))
(org-gnosis--create-file date (expand-file-name file org-gnosis-journal-dir)
(or template org-gnosis-journal-template))))
(define-minor-mode org-gnosis-mode
"Org gnosis mode."
:lighter " org-gnosis"
:keymap nil
:global nil
:group 'org-gnosis
(if org-gnosis-mode
(add-hook 'after-save-hook #'org-gnosis-update-file nil t) ;; buffer local hook
(remove-hook 'after-save-hook #'org-gnosis-update-file)))
;; Org-Gnosis Database
(defconst org-gnosis-db-version 1)
(defconst org-gnosis-db--table-schemata
'((nodes
([(id :not-null :primary-key)
(file :not-null)
(title text)
tags]))
(tags
([(tag-name text :primary-key)]))
(journal
([(id :not-null :primary-key)
(file :not-null)
(date text)
tags]))
;; (node-tags
;; ([(node-id :not-null)
;; (tags :not-null)
;; (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)
;; (:foreign-key [tags] :references tags [tag-name] :on-delete :cascade)]))
(links
([(source text)
(dest text)]
(:foreign-key [source] :references nodes [id] :on-delete :cascade)
))))
(defun org-gnosis-db-delete-tables ()
"Drop all tables."
(ignore-errors
(emacsql-with-transaction org-gnosis-db
(org-gnosis--drop-table 'nodes)
(org-gnosis--drop-table 'tags)
(org-gnosis--drop-table 'journal)
(org-gnosis--drop-table 'links))))
(defun org-gnosis-db-init ()
"Initialize database DB with the correct schema and user version."
(setf org-gnosis-db (emacsql-sqlite-open (locate-user-emacs-file "org-gnosis.db")))
(org-gnosis-db-delete-tables)
(when (length< (emacsql org-gnosis-db
[:select name :from sqlite-master :where (= type table)])
3)
(org-gnosis-db-delete-tables)
(emacsql-with-transaction org-gnosis-db
(pcase-dolist (`(,table ,schema) org-gnosis-db--table-schemata)
(emacsql org-gnosis-db [:create-table $i1 $S2] table schema))
(emacsql org-gnosis-db [:pragma (= user-version org-gnosis-db-version)]))))
(provide 'org-gnosis)
;;; org-gnosis.el ends here
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