path: root/gnosis.el

;;; gnosis.el --- Spaced Repetition Learning Tool  -*- lexical-binding: t; -*-

;; Copyright (C) 2023  Thanos Apollo

;; Author: Thanos Apollo <[email protected]>
;; Keywords: extensions
;; URL: https://git.thanosapollo.org/gnosis
;; Version: 0.0.1

;; Package-Requires: ((emacs "27.2") (compat "29.1.4.2") (emacsql "20230228"))

;; 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:

;; Work in progress

;;; Code:


(require 'emacsql)
(require 'emacsql-sqlite)
(require 'cl-lib)
(require 'gnosis-algorithm)
(require 'gnosis-faces)

(defgroup gnosis nil
  "Spaced repetition learning tool."
  :group 'external
  :prefix "gnosis-")

(defcustom gnosis-dir (concat user-emacs-directory "gnosis")
  "Gnosis directory."
  :type 'directory
  :group 'gnosis)

(defcustom gnosis-cloze-char "__"
  "Gnosis cloze character."
  :type 'string
  :group 'gnosis)


(defvar gnosis-images-dir (concat (file-name-as-directory gnosis-dir) "images")
  "Gnosis images directory.")

(defvar gnosis-db (emacsql-sqlite (concat (file-name-as-directory gnosis-dir) "gnosis.db"))
  "Gnosis database file.

WARNING: Do not change this value!")

(defvar gnosis-testing nil
  "When t, warn user he is in a testing environment.")

(defconst gnosis-db-version 1
  "Gnosis database version.")

(cl-defun gnosis-select (value table &optional (restrictions '1=1))
  "Select VALUE from TABLE, optionally with RESTRICTIONS."
  (gnosis-db-init)
  (emacsql gnosis-db `[:select ,value :from ,table :where ,restrictions]))

(cl-defun gnosis--create-table (table &optional values)
  "Create TABLE for VALUES."
  (emacsql gnosis-db `[:create-table ,table ,values]))

(cl-defun gnosis--drop-table (table)
  "Drop TABLE from gnosis-db."
  (emacsql gnosis-db `[:drop-table ,table]))

(cl-defun gnosis--insert-into (table values)
  "Insert VALUES to TABLE."
  (gnosis-db-init)
  (emacsql gnosis-db `[:insert :into ,table :values ,values]))

(cl-defun gnosis-update (table value where)
  "Update records in TABLE with to new VALUE based on the given WHERE condition.

Example:
 (gnosis-update ='notes ='(= main \"NEW VALUE\") ='(= id 12))"
  (emacsql gnosis-db `[:update ,table :set ,value :where ,where]))

(cl-defun gnosis-get (value table &optional (restrictions '1=1))
  "Return VALUE from TABLE, optionally with where RESTRICTIONS."
  (caar (gnosis-select value table restrictions)))

(defun gnosis-get-note-tags (id)
  "Return tags for note ID."
  (gnosis-get 'tags 'notes `(= id ,id)))

(defun gnosis--delete (table value)
  "From TABLE use where to delete VALUE."
  (emacsql gnosis-db `[:delete :from ,table :where ,value]))

(defmacro with-gnosis-buffer (&rest body)
  "Execute BODY in gnosis buffer."
  `(with-current-buffer (switch-to-buffer (get-buffer-create "*gnosis*"))
     (gnosis-mode)
     ,@body))

(cl-defun gnosis-completing-read (prompt options info &optional (face-for-info 'font-lock-doc-face))
  "A version of `completing-read' with text properties, padding & choosable face.
Returns selected option from OPTIONS.

WARNING: Do NOT use htis functions as is now!

PROMPT is a string to prompt with; normally it ends in a colon and a space.
OPTIONS is a list of strings.
INFO is a list of strings, which will be displayed as additional info for option
FACE-FOR-INFO is the face used to display info for option."
  (let* ((choices (cl-mapcar 'cons options info))
         (max-choice-length (apply 'max (mapcar 'length options)))
         (formatted-choices
          (mapcar (lambda (choice)
                    (cons (concat (format "%s" (car choice))
                                  (make-string (- max-choice-length (length (car choice))) ? )
                                  "      "
                                  (propertize (format "%s" (cdr choice)) 'face face-for-info))
                          (car choice)))
                  choices)))
    (cdr (assoc (completing-read prompt formatted-choices nil t)
		formatted-choices))))

(defun gnosis-replace-item-at-index (index new-item list)
  "Replace item at INDEX in LIST with NEW-ITEM."
  (cl-loop for i from 0 for item in list
           if (= i index) collect new-item
           else collect item))

(defun gnosis-display--question (id)
  "Display main row for note ID."
  (let ((question (gnosis-get 'main 'notes `(= id ,id))))
    (with-gnosis-buffer
     (erase-buffer)
     (fill-paragraph (insert (concat "\n"
				     (propertize question 'face 'gnosis-face-main)))))))

(defun gnosis-display--cloze-sentence (sentence clozes)
  "Display cloze sentence for SENTENCE with CLOZES."
  (with-gnosis-buffer
   (erase-buffer)
   (fill-paragraph
    (insert
     (concat "\n"
	     (gnosis-cloze-replace-words sentence clozes (propertize gnosis-cloze-char 'face 'gnosis-face-cloze)))))))

(defun gnosis-display--basic-answer (answer success user-input)
  "Display ANSWER.

When SUCCESS nil, display USER-INPUT as well"
  (with-gnosis-buffer
   (insert
    (concat "\n\n"
	    (propertize "Answer:" 'face 'gnosis-face-directions)
	    " "
	    (propertize answer 'face 'gnosis-face-correct)))
   ;; Insert user wrong answer
   (when (not success)
     (insert (concat "\n"
		     (propertize "Your answer:" 'face 'gnosis-face-directions)
		     " "
		     (propertize user-input 'face 'gnosis-face-false))))))

(defun gnosis-display--hint (hint)
  "Display HINT."
  (with-gnosis-buffer
   (goto-char (point-max))
   (insert (concat
	    (propertize "\n\n-----\n" 'face 'gnosis-face-seperator)
	    (propertize hint 'face 'gnosis-face-hint)))))

(cl-defun gnosis-display-cloze-reveal (&key (cloze-char gnosis-cloze-char) replace (success t) (face nil))
  "Replace CLOZE-CHAR with REPLACE.

If FACE nil, propertize replace using `gnosis-face-correct', or
`gnosis-face-false' when (not SUCCESS). Else use FACE value."
  (with-gnosis-buffer
   (goto-char (point-min))
   (search-forward cloze-char nil t)
   (replace-match (propertize replace 'face (if (not face)
						(if success 'gnosis-face-correct 'gnosis-face-false)
					      face)))))

(cl-defun gnosis-display-cloze-user-answer (user-input &optional (false t))
  "Display USER-INPUT answer for cloze note upon failed review.

If FALSE t, use gnosis-face-false face"
  (with-gnosis-buffer
   (goto-char (point-max))
   (insert (concat "\n\n"
		   (propertize "Your answer:" 'face 'gnosis-face-directions)
		   " "
		   (propertize user-input 'face (if false 'gnosis-face-false 'gnosis-face-correct))))))

(defun gnosis-display--correct-answer-mcq (answer user-choice)
  "Display correct ANSWER & USER-CHOICE for MCQ note."
  (with-gnosis-buffer
   (insert (concat "\n\n"
		   (propertize "Correct Answer:" 'face 'gnosis-face-directions)
		   " "
		   (propertize answer 'face 'gnosis-face-correct)
		   "\n"
		   (propertize "Your answer:" 'face 'gnosis-face-directions)
		   " "
		   (propertize user-choice 'face (if (string= answer user-choice)
						     'gnosis-face-correct
						   'gnosis-face-false))))))

(defun gnosis-display--extra (id)
  "Display extra information for note ID."
  (let ((extras (gnosis-get 'extra-notes 'extras `(= id ,id))))
    (with-gnosis-buffer
     (goto-char (point-max))
     (insert (propertize "\n\n-----\n" 'face 'gnosis-face-seperator))
     (fill-paragraph (insert (concat "\n" (propertize extras 'face 'gnosis-face-extra)))))))

(defun gnosis-display--image (id)
  "Display image for note ID."
  (let* ((img (gnosis-get 'images 'extras `(= id ,id)))
	 (path-to-image (concat (file-name-as-directory gnosis-images-dir) img))
	 (image (create-image path-to-image 'png nil :width 500 :height 300)))
    (when img
      (with-gnosis-buffer
       (insert "\n\n")
       (insert-image image)))))

(cl-defun gnosis--prompt (prompt &optional (downcase nil) (split nil))
  "PROMPT user for input until `q' is given.

The user is prompted to provide input for the 'PROMPT' message.
Returns the list of non-'q' inputs in reverse order of their entry.

Set DOWNCASE to t to downcase all input given.
Set SPLIT to t to split all input given."
  (cl-loop with input = nil
           for response = (read-string (concat prompt " (q for quit): "))
	   do (if downcase (setf response (downcase response)))
           for response-parts = (if split (split-string response " ") (list response))
           if (member "q" response-parts) return (nreverse input)
           do (cl-loop for part in response-parts
	               unless (string-empty-p part)
                       do (push part input))))

(defun gnosis-add-deck (name)
  "Create deck with NAME."
  (interactive (list (read-string "Deck Name: ")))
  (when gnosis-testing
    (unless (y-or-n-p "You are using a testing environment! Continue?")
      (error "Aborted")))
  (if (gnosis-get 'name 'decks `(= name ,name))
      (error "Deck `%s' already exists" name)
    (gnosis--insert-into 'decks `([nil ,name]))
    (message "Created deck '%s'" name)))

(defun gnosis--get-deck-name ()
  "Return name from table DECKS."
  (when (equal (gnosis-select 'name 'decks) nil)
    (error "No decks found"))
  (completing-read "Deck: " (gnosis-select 'name 'decks)))

(cl-defun gnosis--get-deck-id (&optional (deck (gnosis--get-deck-name)))
  "Return id for DECK name."
  (gnosis-get 'id 'decks `(= name ,deck)))

(defun gnosis-delete-deck (deck)
  "Delete DECK."
  (interactive (list (gnosis--get-deck-name)))
  (gnosis--delete 'decks `(= name ,deck))
  (message "Deleted deck %s" deck))

(defun gnosis-suspend-note (id)
  "Suspend note with ID."
  (gnosis-update 'review-log '(= suspend 1) `(= id ,id)))

(cl-defun gnosis-suspend-deck (&optional (deck (gnosis--get-deck-id)))
  "Suspend all note(s) with DECK id.

When called with a prefix, unsuspends all notes in deck."
  (let ((notes (gnosis-select 'id 'notes `(= deck-id ,deck)))
	(suspend (if current-prefix-arg 0 1))
	(note-count 0))
    (cl-loop for note in notes
	     do (progn (gnosis-update 'review-log `(= suspend ,suspend) `(= id ,(car note)))
		       (setq note-count (1+ note-count)))
	     finally (if (equal suspend 0)
			 (message "Unsuspended %s notes" note-count)
		       (message "Suspended %s notes" note-count)))))

(defun gnosis-suspend-tag ()
  "Suspend all note(s) with tag.

When called with a prefix, unsuspends all notes for tag."
  (let ((notes (gnosis-select-by-tag (gnosis-tag-prompt nil t)))
	(suspend (if current-prefix-arg 0 1)))
    (cl-loop for note in notes
	     do (gnosis-update 'review-log `(= suspend ,suspend) `(= id ,note)))))

(defun gnosis-suspend ()
  "Suspend note(s) with specified values."
  (interactive)
  (let ((item (completing-read "Suspend by: " '("Deck" "Tag"))))
    (pcase item
      ("Deck" (gnosis-suspend-deck))
      ("Tag" (gnosis-suspend-tag))
      (_ (message "Not ready yet.")))))


(defun gnosis-add-note-fields (deck type main options answer extra tags suspend image second-image)
  "Add fields for new note.

DECK: Deck for new note.
TYPE: Note type e.g \"mcq\"
MAIN: Note's main part
OPTIONS: Note's options, e.g choices for mcq for OR hints for
cloze/basic type
ANSWER: Correct answer for note, for MCQ is an integer while for
cloze/basic a string/list of the right answer(s)
EXTRA: Extra information to display after answering note
TAGS: Tags to organize notes
SUSPEND: Integer value of 1 or 0, where 1 suspends the card
IMAGE: Image to display during review.
SECOND-IMAGE: Image to display after user-input."
  (gnosis--insert-into 'notes `([nil ,type ,main ,options ,answer ,tags ,(gnosis--get-deck-id deck)]))
  (gnosis--insert-into 'review `([nil ,gnosis-algorithm-ef ,gnosis-algorithm-ff ,gnosis-algorithm-interval]))
  (gnosis--insert-into 'review-log `([nil ,(gnosis-algorithm-date) ,(gnosis-algorithm-date) 0 0 0 0 ,suspend 0]))
  (gnosis--insert-into 'extras `([nil ,extra ,image ,second-image])))


;; Adding note(s) consists firstly of a hidden 'gnosis-add-note--TYPE'
;; function that does the computation & error checking to generate a
;; note from given input. Secondly, 'gnosis-add-note-TYPE' normal
;; function, which prompts for user input and passes it to the hidden
;; function.

(cl-defun gnosis-add-note--mcq (&key deck question choices correct-answer
				     extra (image nil) tags (suspend 0) (second-image nil))
  "Create a NOTE with a list of multiple CHOICES.

MCQ type consists of a main `QUESTION' that is displayed to the user.
The user will be prompted to select the correct answer from a list of
`CHOICES'. The `CORRECT-ANSWER' should be the index of the correct
choice in the `CHOICES' list. Each note must correspond to one `DECK'.

`IMAGE' Image to display before user-input
`SECOND-IMAGE' Image to display after user-input
`EXTRA' are extra information displayed after an answer is given.
`TAGS' are used to organize questions.
`SUSPEND' is a binary value, where 1 is for suspend."
  (cond ((or (not (numberp correct-answer)) (equal correct-answer 0))
	 (error "Correct answer value must be the index number of the correct answer"))
	((null tags)
	 (setf tags 'untagged)))
  (gnosis-add-note-fields deck "mcq" question choices correct-answer extra tags suspend image second-image))

(defun gnosis-add-note-mcq ()
  "Add note(s) of type `MCQ' interactively to selected deck.

Create a note type MCQ for specified deck, that consists of:
STEM: The question or problem statement
OPTIONS: Options for the user to select
ANSWER: Answer is the NUMBER of the correct answer of OPTIONS.
EXTRA: Information to display after user-input
TAGS: Used to organize notes

Refer to `gnosis-add-note--mcq' for more."
  (let ((deck (gnosis--get-deck-name)))
    (while (y-or-n-p (format "Add note of type `MCQ' to `%s' deck? " deck))
      (gnosis-add-note--mcq :deck deck
			    :question (read-string "Question: ")
			    :choices (gnosis--prompt "Choices")
			    :correct-answer (string-to-number (read-string "Which is the correct answer (number)? "))
			    :extra (read-string "Extra: ")
			    :tags (gnosis-tag-prompt)))))

(cl-defun gnosis-add-note--basic (&key deck question hint answer
				       extra (image nil) tags (suspend 0) (second-image nil))
  "Add Basic type note.

DECK: Deck name for note.
QUESTION: Quesiton to display for note.
ANSWER: Answer for QUESTION, which user will be prompted to type
HINT: Hint to display during review, before user-input.
EXTRA: Extra information to display after user-input/giving an answer.
IMAGE: Image to display before user-input.
TAGS: Tags used to organize notes
SUSPEND: Binary value of 0 & 1, when 1 note will be ignored."
  (gnosis-add-note-fields deck "basic" question hint answer extra tags suspend image second-image))

(defun gnosis-add-note-basic ()
  "Add note(s) of type `Basic' interactively to selected deck.

Basic note type is a flashcard-like note, where user first sees a
\"main\" part, which is usually a question, and he is prompted to
input the answer.

Refer to `gnosis-add-note--basic' for more."
  (let ((deck (gnosis--get-deck-name)))
    (while (y-or-n-p (format "Add note of type `basic' to `%s' deck? " deck))
      (gnosis-add-note--basic :deck deck
			      :question (read-string "Question: ")
			      :answer (read-string "Answer: ")
			      :hint (read-string "Hint: ")
			      :extra (read-string "Extra: ")
			      :tags (gnosis-tag-prompt)))))

(cl-defun gnosis-add-note--double (&key deck question hint answer extra (image nil) tags (suspend 0) (second-image nil))
  "Add Double type note.

Essentially, a \"note\" that generates 2 basic notes. The second one
reverses question/answer.

DECK: Deck name for note.
QUESTION: Quesiton to display for note.
ANSWER: Answer for QUESTION, which user will be prompted to type
HINT: Hint to display during review, before user-input.
EXTRA: Extra information to display after user-input/giving an answer.
IMAGE: Image to display before user-input.
TAGS: Tags used to organize notes
SUSPEND: Binary value of 0 & 1, when 1 note will be ignored."
  (gnosis-add-note-fields deck "basic" question hint answer extra tags suspend image second-image)
  (gnosis-add-note-fields deck "basic" answer hint question extra tags suspend image second-image))

(defun gnosis-add-note-double ()
  "Add note(s) of type double interactively to selected deck.

Essentially, a \"note\" that generates 2 basic notes. The second one
reverses question/answer.

Refer to `gnosis-add-note--double' for more."
  (let ((deck (gnosis--get-deck-name)))
    (while (y-or-n-p (format "Add note of type `double' to `%s' deck? " deck))
      (gnosis-add-note--double :deck deck
			       :question (read-string "Question: ")
			       :answer (read-string "Answer: ")
			       :image (when (y-or-n-p "Add image to display during review?")
					(completing-read "Select image: " (gnosis-directory-files)))
			       :hint (read-string "Hint: ")
			       :extra (read-string "Extra: ")
			       :tags (gnosis-tag-prompt)))))

(cl-defun gnosis-add-note--cloze (&key deck note hint tags (suspend 0) extra (image nil) (second-image nil))
  "Add cloze type note.

DECK: Deck name for note.
NOTE: Note with clozes, format for clozes is as follows:
      This is a {c1:cloze} note type.
      This is a {{c1::cloze}} note type.

Anki like syntax is supported with double brackes and colon, as well
as single brackets({}) and colon(:), or even a mix.

For each cX: tag, there will be gerenated a cloze note type.
Example:
      {c1:Preformed enterotoxins} from
      {c2:Staphylococcus aureus} causes {c3:rapid} onset
      food poisoning

Generates 3 cloze note types. Where the \"main\" part of the note is the full
note, with the cloze(s) extracted & used as the \"answer\".

One cloze note may have multiple clozes
Example:
      {c1:Streptococcus agalactiae (GBS)} and {c1:Listeria
      monocytogenes} are CAMP test positive
   
HINT: Hint to display during review, before user-input.
   NOTE! In gnosis-db, hint is referred to as `options', same column options used in mcq.
IMAGE: Image to display before user-input.
TAGS: Tags used to organize notes
SUSPEND: When t, note will be ignored.
EXTRA: Extra information displayed after user-input.
SECOND-IMAGE: Image to display after user-input."
  (let ((notags-note (gnosis-cloze-remove-tags note))
	(clozes (gnosis-cloze-extract-answers note)))
    (cl-loop for cloze in clozes
	     do (gnosis-add-note-fields deck "cloze" notags-note hint cloze extra tags suspend image second-image))))

(defun gnosis-add-note-cloze ()
  "Add note(s) of type cloze interactively to selected deck.

Note with clozes, format for clozes is as follows:
      This is a {c1:cloze} note type.
      This is a {{c1::cloze}} note type.

Anki like syntax is supported with double brackes and colon, as well
as single brackets({}) and colon(:), or even a mix.

One cloze note may have multiple clozes
Example:
      {c1:Streptococcus agalactiae (GBS)} and {c1:Listeria
      monocytogenes} are CAMP test positive

For each cX: tag, there will be gerenated a cloze note type.
Example:
      {c1:Preformed enterotoxins} from
      {c2:Staphylococcus aureus} causes {c3:rapid} onset
      food poisoning

Generates 3 cloze note types. Where the \"main\" part of the note is
the full note, with the cloze(s) extracted & used as the \"answer\".

See `gnosis-add-note--cloze' for more reference."
  (let ((deck (gnosis--get-deck-name)))
    (while (y-or-n-p (format "Add note of type `cloze' to `%s' deck? " deck))
      (gnosis-add-note--cloze :deck deck
			      :note (read-string "Question: ")
			      :hint (read-string "Hint: ")
			      :extra (read-string "Extra: ")
			      :tags (gnosis-tag-prompt)))))

;;;###autoload
(defun gnosis-add-note (type)
  "Create note(s) as TYPE interactively."
  (interactive (list (completing-read "Type: " '(MCQ Cloze Basic Double) nil t)))
  (when gnosis-testing
    (unless (y-or-n-p "You are using a testing environment! Continue?")
      (error "Aborted")))
  (pcase type
    ("MCQ" (gnosis-add-note-mcq))
    ("Cloze" (gnosis-add-note-cloze))
    ("Basic" (gnosis-add-note-basic))
    ("Double" (gnosis-add-note-double))
    (_ (message "No such type."))))

(defun gnosis-export-deck (deck filename)
  "Export DECK as FILENAME.

Export all notes for DECK, in a file as FILENAME."
  (interactive (list (gnosis--get-deck-id)
		     (read-string "Name for exported file: ")))
  (let ((notes (gnosis-select '[type main options answer tags] 'notes `(= deck-id ,deck)))
	(default-directory gnosis-dir))
    (with-temp-file (concat filename ".el")
      (insert "(" (concat "gnosis-define-deck " "'" filename "\n"))
      (insert (pp-to-string notes) "\n")
      (insert ")" ))))

(defun gnosis-mcq-answer (id)
  "Choose the correct answer, from mcq choices for question ID."
  (let ((choices (gnosis-get 'options 'notes `(= id ,id)))
	(history-add-new-input nil)) ;; Disable history
    (completing-read "Answer: " choices)))

(defun gnosis-cloze-remove-tags (string)
  "Replace cx-tags in STRING.

Works both with {} and {{}} to make easier to import anki notes."
  (let* ((regex "{\\{1,2\\}c\\([0-9]+\\)::?\\(.*?\\)}\\{1,2\\}")
         (result (replace-regexp-in-string regex "\\2" string)))
    result))

(defun gnosis-cloze-replace-words (string words new)
  "In STRING replace WORDS with NEW."
  (cl-assert (listp words))
  (cl-loop for word
	   in words
	   do (setf string (replace-regexp-in-string (concat "\\<" word "\\>") ;; use word boundary indentifiers
						     new string)))
  string)

(defun gnosis-cloze-extract-answers (str)
  "Extract cloze answers for STR.

Return a list of cloze answers for STR, organized by cX-tag.

Valid cloze formats include:
\"This is an {c1:example}\"
\"This is an {c1::example}\"
\"This is an {{c1:example}}\"
\"This is an {{c1::example}}\""
  (let ((result-alist '())
        (start 0))
    (while (string-match "{\\{1,2\\}c\\([0-9]+\\)::?\\(.*?\\)}\\{1,2\\}" str start)
      (let* ((tag (match-string 1 str))
             (content (match-string 2 str)))
        (if (assoc tag result-alist)
            (push content (cdr (assoc tag result-alist)))
          (push (cons tag (list content)) result-alist))
        (setf start (match-end 0))))
    (mapcar (lambda (tag-group) (nreverse (cdr tag-group)))
	    (nreverse result-alist))))

(defun gnosis-compare-strings (str1 str2)
  "Compare STR1 and STR2.

Compare 2 strings, ignoring case and whitespace."
  (let ((modified-str1 (downcase (replace-regexp-in-string "\\s-" "" str1)))
        (modified-str2 (downcase (replace-regexp-in-string "\\s-" "" str2))))
    (string= modified-str1 modified-str2)))

(defun gnosis-directory-files (&optional dir regex)
  "Return a list of file paths, relative to DIR directory.

DIR is the base directory path from which to start the recursive search.
REGEX is the regular expression pattern to match the file names against.

This function traverses the subdirectories of DIR recursively,
collecting file paths that match the regular expression. The file
paths are returned as a list of strings, with each string representing
a relative file path to DIR.

By default, DIR value is `gnosis-images-dir' & REGEX value is \"^[^.]\""
  (let ((dir (or dir gnosis-images-dir))
	(regex (or regex "^[^.]")))
    (apply #'append
           (cl-loop for path in (directory-files dir t directory-files-no-dot-files-regexp)
                    if (file-directory-p path)
                    collect (mapcar (lambda (file) (concat (file-relative-name path dir) "/" file))
                                    (gnosis-directory-files path regex))
                    else if (string-match-p regex (file-name-nondirectory path))
                    collect (list (file-relative-name path dir))))))

(defun gnosis-select-image (&optional prompt)
  "Return PATH for file in `gnosis-images-dir'.

Optionally, add cusotm PROMPT."
  (let* ((prompt (or prompt "Select image: "))
	 (image (completing-read prompt (gnosis-directory-files gnosis-images-dir))))
    image))

(defun gnosis-get-tags--unique ()
  "Return a list of unique strings for tags in gnosis-db."
  (cl-loop for tags in (gnosis-select 'tags 'notes)
           nconc tags into all-tags
           finally return (delete-dups all-tags)))

(defun gnosis-select-by-tag (input-tags)
  "Return note id for every note with INPUT-TAGS."
  (unless (listp input-tags)
    (error "`input-tags' need to be a list"))
  (cl-loop for (id tags) in (emacsql gnosis-db [:select [id tags] :from notes])
           when (and (cl-every (lambda (tag) (member tag tags)) input-tags)
		     (not (gnosis-suspended-p id)))
           collect id))

(defun gnosis-suspended-p (id)
  "Return t if note with ID is suspended."
  (if (= (gnosis-get 'suspend 'review-log `(= id ,id)) 1)
      t
    nil))

(defun gnosis-tag-prompt (&optional prompt match)
  "PROMPT user to select tags, until they enter `q'.
Prompt user to select tags, generated from `gnosis-get-tags--unique'.

PROMPT: Prompt string value
MATCH: Require match, t or nil value

Returns a list of unique tags."
  (let* ((tags '())
         (tag "")
	 (prompt (or prompt "Selected tags"))
	 (match (or match nil)))
    (while (not (string= tag "q"))
      (setf tag (completing-read (concat prompt (format " %s (q for quit): " tags))
				 (cons "q" (gnosis-get-tags--unique)) nil match))
      (unless (or (string= tag "q") (member tag tags))
        (push tag tags)))
    (reverse tags)))

;; Review
;;;;;;;;;;
(defun gnosis-review--algorithm (id success)
  "Return next review date & ef for note with value of id ID.

SUCCESS is a binary value, 1 = success, 0 = failure.
Returns a list of the form ((yyyy mm dd) ef)."
  (let ((ff gnosis-algorithm-ff)
	(ef (nth 2 (gnosis-get 'ef 'review `(= id ,id))))
	(c-success (gnosis-get 'c-success 'review-log `(= id ,id))))
    (gnosis-algorithm-next-interval (gnosis-review--get-offset id)
				    (gnosis-get 'n 'review-log `(= id ,id))
				    ef success ff c-success)))

(defun gnosis-review-is-due-p (note-id)
  "Return t if unsuspended note with NOTE-ID is due today."
  (emacsql gnosis-db `[:select [id] :from review-log :where (and (<= next-rev ',(gnosis-algorithm-date))
								 (= suspend 0)
								 (= id ,note-id))]))

(defun gnosis-review-get-due-notes ()
  "Return a list due notes id for current date.

Select notes where:
 - Next review date <= current date
 - Not suspended."
  (apply #'append
	 (emacsql gnosis-db `[:select [id] :from review-log :where (and (<= next-rev ',(gnosis-algorithm-date))
								 (= suspend 0))])))

(defun gnosis-review-due-notes--with-tags ()
  "Return a list of due note tags."
  (let ((due-notes (gnosis-review-get-due-notes)))
    (cl-remove-duplicates
     (cl-mapcan (lambda (note-id)
                  (gnosis-get-note-tags note-id))
	        due-notes)
     :test 'equal)))

(defun gnosis-review--get-offset (id)
  "Return offset for note with value of id ID."
  (let ((last-rev (gnosis-get 'last-rev 'review-log `(= id ,id))))
    (gnosis-algorithm-date-diff last-rev)))

(defun gnosis-review-round (num)
  "Round NUM to 1 decimal.

This function is used to round floating point numbers to 1 decimal,
such as the easiness factor (ef)."
  (/ (round (* num 100.00)) 100.00))

(defun gnosis-review-new-ef (id success)
  "Return new ef for note with value of id ID.

SUCCESS is a binary value, 1 = success, 0 = failure.
Returns a list of the form (ef-increase ef-decrease ef)."
  (let ((ef (nth 1 (gnosis-review--algorithm id success)))
	(old-ef (gnosis-get 'ef 'review `(= id ,id))))
    (cl-substitute (gnosis-review-round ef) (nth 2 old-ef) old-ef)))

(defun gnosis-review--update (id success)
  "Update review-log for note with value of id ID.

SUCCESS is a binary value, 1 is for successful review."
  (let ((ef (gnosis-review-new-ef id 1)))
    ;; Update review-log
    (gnosis-update 'review-log `(= last-rev ',(gnosis-algorithm-date)) `(= id ,id))
    (gnosis-update 'review-log `(= next-rev ',(car (gnosis-review--algorithm id success))) `(= id ,id))
    (gnosis-update 'review-log `(= n (+ 1 ,(gnosis-get 'n 'review-log `(= id ,id)))) `(= id ,id))
    ;; Update review
    (gnosis-update 'review `(= ef ',ef) `(= id ,id))
    (if (= success 1)
	(progn (gnosis-update 'review-log `(= c-success ,(1+ (gnosis-get 'c-success 'review-log `(= id ,id)))) `(= id ,id))
	       (gnosis-update 'review-log `(= t-success ,(1+ (gnosis-get 't-success 'review-log `(= id ,id)))) `(= id ,id))
	       (gnosis-update 'review-log `(= c-fails 0) `(= id ,id)))
      (gnosis-update 'review-log `(= c-fails ,(1+ (gnosis-get 'c-fails 'review-log `(= id ,id)))) `(= id ,id))
      (gnosis-update 'review-log `(= t-fails ,(1+ (gnosis-get 't-fails 'review-log `(= id ,id)))) `(= id ,id))
      (gnosis-update 'review-log `(= c-success 0) `(= id ,id)))))

(defun gnosis-review-mcq (id)
  "Display multiple choice answers for question ID."
  (gnosis-display--image id)
  (gnosis-display--question id)
  (let* ((choices (gnosis-get 'options 'notes `(= id ,id)))
	 (answer (nth (- (gnosis-get 'answer 'notes `(= id ,id)) 1) choices))
	 (user-choice (gnosis-mcq-answer id)))
    (if (string= answer user-choice)
        (progn (gnosis-review--update id 1)
	       (message "Correct!"))
      (gnosis-review--update id 0)
      (message "False"))
    (gnosis-display--correct-answer-mcq answer user-choice)
    (gnosis-display--extra id)))

(defun gnosis-review-basic (id)
  "Review basic type note for ID."
  (gnosis-display--image id)
  (gnosis-display--question id)
  (gnosis-display--hint (gnosis-get 'options 'notes `(= id ,id)))
  (let* ((answer (gnosis-get 'answer 'notes `(= id ,id)))
	 (user-input (read-string "Answer: "))
	 (success (gnosis-compare-strings answer user-input)))
    (gnosis-display--basic-answer answer success user-input)
    (gnosis-display--extra id)
    (gnosis-review--update id (if success 1 0))))

(defun gnosis-review-cloze--input (cloze)
  "Prompt for user input during cloze review.

If user-input is equal to CLOZE, return t."
  (let ((user-input (read-string "Answer: ")))
    (cons (gnosis-compare-strings user-input cloze) user-input)))

(defun gnosis-review-cloze-reveal-unaswered (clozes)
  "Reveal CLOZES.

Used to reveal all clozes left with `gnosis-face-cloze-unanswered' face."
  (cl-loop for cloze in clozes do (gnosis-display-cloze-reveal :replace cloze
							       :face 'gnosis-face-cloze-unanswered)))

(defun gnosis-review-cloze (id)
  "Review cloze type note for ID."
  (let* ((main (gnosis-get 'main 'notes `(= id ,id)))
	 (clozes (gnosis-get 'answer 'notes `(= id ,id)))
	 (num 1)
	 (clozes-num (length clozes))
	 (hint (gnosis-get 'options 'notes `(= id ,id))))
    (gnosis-display--image id)
    (gnosis-display--cloze-sentence main clozes)
    (gnosis-display--hint hint)
    (cl-loop for cloze in clozes
	     do (let ((input (gnosis-review-cloze--input cloze)))
		  (if (equal (car input) t)
		      ;; Reveal only one cloze
		      (progn (gnosis-display-cloze-reveal :replace cloze)
			     (setf num (1+ num)))
		    ;; Reveal cloze for wrong input, with `gnosis-face-false'
		    (gnosis-display-cloze-reveal :replace cloze :success nil)
		    ;; Do NOT remove the _when_ statement, unexpected
		    ;; bugs occur if so depending on the number of
		    ;; clozes.
		    (when (< num clozes-num) (gnosis-review-cloze-reveal-unaswered clozes))
		    (gnosis-display-cloze-user-answer (cdr input))
		    (gnosis-review--update id 0)
		    (cl-return)))
	     finally (gnosis-review--update id 1)))
  (gnosis-display--extra id))

(defun gnosis-review-note (id)
  "Start review for note with value of id ID, if note is unsuspended."
  (cond ((gnosis-suspended-p id)
         (message "Note is suspended."))
        (t
         (let ((type (gnosis-get 'type 'notes `(= id ,id))))
           (pcase type
             ("mcq" (gnosis-review-mcq id))
             ("basic" (gnosis-review-basic id))
             ("cloze" (gnosis-review-cloze id))
             (_ (error "Malformed note type")))))))

(defun gnosis-review-commit (note-num)
  "Commit review session on git repository.

This function initializes the `gnosis-dir' as a Git repository if it is not
already one. It then adds the gnosis.db file to the repository and commits
the changes with a message containing the review type and the number of notes.

TYPE: The type of the review session.
NOTE-NUM: The number of notes reviewed in the session."
  (let ((git (executable-find "git"))
	(default-directory gnosis-dir))
    (unless git
      (error "Git not found, please install git"))
    (unless (file-exists-p (concat (file-name-as-directory gnosis-dir) ".git"))
      (shell-command "git init"))
    (sit-for 0.2)
    (shell-command (concat git " add " (shell-quote-argument "gnosis.db")))
    (shell-command (concat git " commit -m "
			   (shell-quote-argument (concat (format "Total notes for session: %d " note-num)))))
    (message "Review session finished. %d notes reviewed." note-num)))

(defun gnosis-review--session (notes)
  "Start review session for NOTES."
  (when (null notes)
    (message "No due notes."))
  (let ((note-count 0))
    (when (y-or-n-p (format "You have %s total notes for review, start session?" (length notes)))
      (cl-loop for note in notes
	       do (progn (gnosis-review-note note)
			 (setf note-count (1+ note-count))
			 (pcase (read-char-choice "Note Action: [n]ext, [s]uspend, [e]dit, [q]uit: " '(?n ?s ?e ?q))
			   (?n nil)
			   (?s (gnosis-suspend-note note))
			   (?e (progn (gnosis-edit-note note)
				      (recursive-edit)))
			   (?q (progn (gnosis-review-commit note-count)
				      (cl-return)))))
	       finally (gnosis-review-commit note-count)))))


;; Editing notes

(defun gnosis-edit-note (id)
  "Edit note with value of id ID."
  (pcase (completing-read "Edit: " '(contents ef) nil t)
    ("contents" (gnosis-edit-note-contents id))
    ("ef" (gnosis-edit-ef id))
    (_ (message "No such value."))))

(defun gnosis-edit-ef (id)
  "Edit easiness factor values for note with id value ID."
  (let ((ef-full (caar (gnosis-select 'ef 'review `(= id ,id))))
	(old-value-index (pcase (completing-read "Change Factor: " '("Increase" "Decrease" "Total"))
			   ("Total" 2)
			   ("Decrease" 1)
			   ("Increase" 0)))
	(new-value (float (string-to-number (read-string "New value: ")))))
    ;; error checking.
    (cond ((>= 0 new-value) (error "New value needs to be a number & higher than `0'"))
	  ;; Check if when total-ef is selected, new value is higher than 1.3
	  ((and (>= 1.3 new-value) (= old-value-index 2) (error "New total ef needs to be higher than `1.3'"))))
    ;; Use `gnosis-replace-item-at-index' to generate new list with
    ;; new ef value. Change ef value at gnosis-db using
    ;; `gnosis-update'
    (gnosis-update 'review `(= ef ',(gnosis-replace-item-at-index old-value-index new-value ef-full)) `(= id ,id))))

;;;###autoload
(defun gnosis-review ()
  "Start gnosis review session."
  (interactive)
  (gnosis-db-init)
  (let ((review-type (completing-read "Review: " '("Due notes"
						   "Due notes of specified tag(s)"
						   "Notes with tag(s)"))))
    (pcase review-type
      ("Due notes" (gnosis-review--session (gnosis-review-get-due-notes)))
      ("Due notes of specified tag(s)" (gnosis-review--session
					(gnosis-select-by-tag
					 (list (completing-read "Start session for tag: "
								(gnosis-review-due-notes--with-tags))))))
      ("Notes with tag(s)" (gnosis-review--session (gnosis-select-by-tag (gnosis-tag-prompt nil t)))))))

;;; Database Schemas
(defvar gnosis-db-schema-decks '([(id integer :primary-key :autoincrement)
				  (name text :not-null)]))

(defvar gnosis-db-schema-notes '([(id integer :primary-key :autoincrement)
				  (type text :not-null)
				  (main text :not-null)
				  (options text :not-null)
				  (answer text :not-null)
				  (tags text :default untagged)
				  (deck-id integer :not-null)]
				 (:foreign-key [deck-id] :references decks [id]
					       :on-delete :cascade)))

(defvar gnosis-db-schema-review '([(id integer :primary-key :not-null) ;; note-id
				   (ef integer :not-null) ;; Easiness factor
				   (ff integer :not-null) ;; Forgetting factor
				   (interval integer :not-null)] ;; Interval
				  (:foreign-key [id] :references notes [id]
						:on-delete :cascade)))

(defvar gnosis-db-schema-review-log '([(id integer :primary-key :not-null) ;; note-id
				       (last-rev integer :not-null)  ;; Last review date
				       (next-rev integer :not-null)  ;; Next review date
				       (c-success integer :not-null) ;; number of consecutive successful reviews
				       (t-success integer :not-null) ;; Number of total successful reviews
				       (c-fails integer :not-null)   ;; Number of consecutive failed reviewss
				       (t-fails integer :not-null)   ;; Number of total failed reviews
				       (suspend integer :not-null)   ;; Binary value, 1=suspended
				       (n integer :not-null)]        ;; Number of reviews
				      (:foreign-key [id] :references notes [id]
						    :on-delete :cascade)))

(defvar gnosis-db-schema-extras '([(id integer :primary-key :not-null)
				   (extra-notes string)
				   (images string)
				   (extra-image string)]
				  (:foreign-key [id] :references notes [id]
						:on-delete :cascade)))

(defun gnosis-db-init ()
  "Create gnosis essential directories & database."
  ;; Create gnosis-dir
  (unless (file-exists-p gnosis-dir)
    (make-directory gnosis-dir)
    (make-directory gnosis-images-dir)
    ;; Make sure gnosis-db is initialized
    (setf gnosis-db (emacsql-sqlite (concat (file-name-as-directory gnosis-dir) "gnosis.db"))))
  ;; Create database tables
  (unless (length= (emacsql gnosis-db [:select name :from sqlite-master :where (= type table)]) 6)
    ;; Enable foreign keys
    (emacsql gnosis-db "PRAGMA foreign_keys = ON")
    ;; Gnosis version
    (emacsql gnosis-db (format "PRAGMA user_version = %s" gnosis-db-version))
    ;; Create decks table
    (gnosis--create-table 'decks gnosis-db-schema-decks)
    ;; Create notes table
    (gnosis--create-table 'notes gnosis-db-schema-notes)
    ;; Create review table
    (gnosis--create-table 'review gnosis-db-schema-review)
    ;; Create review-log table
    (gnosis--create-table 'review-log gnosis-db-schema-review-log)
    ;; Create extras table
    (gnosis--create-table 'extras gnosis-db-schema-extras)))

;; Gnosis mode ;;
;;;;;;;;;;;;;;;;;

(define-derived-mode gnosis-mode special-mode "Gnosis"
  "Gnosis Mode."
  :interactive t
  (read-only-mode 0)
  (display-line-numbers-mode 0)
  :lighter " gnosis-mode")


(provide 'gnosis)
;;; gnosis.el ends here