md-roam.el

;;; md-roam.el --- description -*- lexical-binding: t; -*-
;;
;; Copyright (C) 2020-2024 Noboru Ota
;;
;; Author: Noboru Ota <https://github.com/nobiot>
;; URL: https://github.com/nobiot/md-roam
;; Version: 2.0.1
;; Last modified: 2024-01-17T234302
;; Package-Requires: ((emacs "27.1") (org-roam "2.1.0") (markdown-mode "2.5"))
;; Keywords: markdown, zettelkasten, note-taking, writing, org, org-roam

;; This file is not part of GNU Emacs.

;; 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 <http://www.gnu.org/licenses/>.

;;; Commentary:

;;  Use org-roam with markdown files by adding md-roam to it.  md-roam extends
;;  the features and functions provided by org-roam to support markdown files
;;  in addition to org

;;  Refer to README in the GitHub repo for instruction, configuraiton,
;;  and features supported in more detail

;;; Code:

;;;; Requirements

(eval-when-compile (require 'subr-x))
;; Markdown
(require 'markdown-mode)
;; Org
(require 'org)
(require 'ol)
(require 'org-macs)
;; Org-roam and its prequisites directly used by Md-roam
(require 'org-roam)
(require 'org-roam-db)
(require 'org-roam-utils)
(require 'emacsql)

;;;; Customization

(defgroup md-roam nil
  "Use markdown files in Org-roam."
  :group 'org-roam
  :prefix "md-roam-"
  :link '(url-link :tag "Github" "https://github.com/nobiot/md-roam"))

(defcustom md-roam-file-extension "md"
  "Define the extesion to be used for Md-roam within Org-roam directory.
Unlike 'org-roam-file-extension', this is a single value, not a list.
It is intended to be used for you to define a different markdown extension,
such as .md and .markdown."
  :group 'md-roam
  :type '(choice
          (string)
          (repeat :tag "List of extensions (string)" string)))

(defcustom md-roam-node-insert-type 'title-or-alias
  "Define whether ID or title/aliase should be inserted.
This is for `md-roam-node-insert'.  If 'title-and-alias, the
resultant wiki link will be \"[[title]]\.  If 'ID, it will be
\"[[ID]] title\"."
  :type '(choice (const :tag "Title or alias" title-or-alias)
                 (const :tag "Node ID" id))
  :group 'md-roam)

;;;; Variables

(defvar md-roam-db-compatible-version 18
  "`Compatible 'org-roam-db-version'.
This is as described in \(info \"(org-roam\)Developer's Guide to Org-roam\"\).")

;;;; These regular expressions are modified version of
;;;; `markdown-regex-yaml-metadata-border.
;;;; I am adding "^" to indicate that the a line needs to
;;;; start with the delineator.

(defvar md-roam-regex-yaml-font-matter-beginning
  "\\(^-\\{3\\}\\)$"
  "Regexp for the beginning of YAML front matter section.
In `markdown-mode', beginning and ending are the same: \"---\".")

(defvar md-roam-regex-yaml-font-matter-ending
  "\\(^-\\{3\\}\\)$"
  "Regexp for the ending of YAML front matter section.
Separate regular expressions for beginning and ending are defined
here because in some markdown conventions, the ending is
delineated by \"```\".

This can be potentially supported setting a custom regexp for
the ending delineator.

If you change this to `\\(^`'\\{3\\}\\)$', you should be able to
support YAML matter ending with ```. I am not testing it, though.")

(defvar md-roam-regex-title
  "\\(^title:[ \t]*\\)\\(.*\\)")

(defvar md-roam-regex-id
  "\\(^id:[ \t]*\\)\\(.*\\)")

(defvar md-roam-regex-aliases
  ;; Assumed to be case insensitive
  "\\(^.*ROAM_ALIASES:[ \t]*\\)\\(.*\\)")

(defvar md-roam-regex-ref-keys
  ;; Assumed to be case insensitive
  "\\(^.*ROAM_REFS:[ \t]*\\)\\(.*\\)")

(defvar md-roam-regex-headline
  (concat "^\s*\n"                   ;exludes YAML front matter
          "\\(.*$\\)\n\\(^[=-]+$\\)" ;heading with '=' and '-'
          "\\|"                      ;regex 'or'
          "\\(^#+ \\)\\(.*$\\)"))    ;heading with '#'

(defvar md-roam-regex-in-text-citation-2
  "\\(?:[^[:alnum:]]\\|^\\)\\(-?@\\)\\([-a-zA-Z0-9_+:]+\\)"
  "Regular expression for stand-alone citation with no anchor.
Regexp for pandoc style citation for link extraction
Copy from pandco-mode to remove dependency

[@bibkey], [@bibkey1, xx; bibkey2, yy]
https://pandoc.org/MANUAL.html#citations

Blah blah [see @doe99, pp. 33-35; also @smith04, chap. 1].
Blah blah [@doe99, pp. 33-35, 38-39 and *passim*].
Blah blah [@smith04; @doe99].
[@smith{ii, A, D-Z}, with a suffix]
[@smith, {pp. iv, vi-xi, (xv)-(xvii)} with suffix here]

A minus sign (-) before the @ will suppress mention

Smith says blah [-@smith04].

in-text citation:

@smith04 says blah.

@smith04 [p. 33] says blah.

With my testing, citation-2 can detect all the cases for md-roam")

(defvar md-roam-regex-tags-zettlr-style
  "\\([^/s]\\)\\([#@][[:alnum:]_-]+\\)"
  "Regexp for extracting tags.
This regexp is intended to be compatible with Zettlr:

     `#tag1 #tag-with-hyphen #tag_with_underscore'

Note that iA Writer treats hyphen (-) as a word delimiter
within a tag.  That is, iA Writer treats #tag-hyphen tagged as
#tag, and ignores `-hyphen'.

If iA Writer's stricter style is preferred, the regexp should
be defined as:

     `\\([^/s]\\)\\([#@][[:alnum:]_]+\\)'")

(defconst md-roam-regex-link-inline
  "\\(?1:!\\)?\\(?2:\\[\\)\\(?3:\\^?\\(?:\\\\\\]\\|[^]]\\)*\\|\\)\\(?4:\\]\\)\\(?5:(\\)\\(?6:[^)]*?\\)\\(?:\\s-+\\(?7:\"[^\"]*\"\\)\\)?\\(?8:)\\)"
  "Copy of `markdown-regex-link-inline' from Markdown Mode.
Regexp for inline links [description](link) and images ![description](link).

Regular expression for a [text](file) or an image link ![text](file).
Group 1 matches the leading exclamation point (optional).
Group 2 matches the opening square bracket.
Group 3 matches the text inside the square brackets.
Group 4 matches the closing square bracket.
Group 5 matches the opening parenthesis.
Group 6 matches the URL.
Group 7 matches the title (optional).
Group 8 matches the closing parenthesis.")

;;;; Commands

;;;###autoload
(define-minor-mode md-roam-mode
  "Md-roam mode needs to be turned before `org-roam-db-sync'.
It needs to be turned on before `org-roam-db-autosync-mode'."
  :init-value nil
  :lighter "md-roam"
  :global t
  (cond
   (md-roam-mode
    ;; Check org-roam-db-version
    ;; This is as described in (info "(org-roam)Developer's Guide to Org-roam")
    (if (not (eq org-roam-db-version md-roam-db-compatible-version))
        (progn
          (message (format "Md-roam not turned on; `org-roam-db-version' %d is not compatible" org-roam-db-version))
          (setq md-roam-mode nil))
      ;; Org-roam cache
      (advice-add #'org-roam-db-update-file :before-until #'md-roam-db-update-file)
      ;; Other interactive commands
      (advice-add #'org-roam-node-insert :before-until #'md-roam-node-insert)
      (advice-add #'markdown-follow-wiki-link :before-until #'md-roam-follow-wiki-link)
      ;; This avoids capture process to add ID in the Org property drawer
      (add-hook 'org-roam-capture-preface-hook #'md-roam-capture-preface)
      (advice-add #'org-id-get :before-until #'md-roam-id-get)
      (advice-add #'org-roam-id-at-point :before-until #'md-roam-id-at-point)
      ;; `org-roam-mode' buffer
      (advice-add #'org-roam-node-at-point
                  :before-until #'md-roam-node-at-point)
      (advice-add #'org-roam-preview-get-contents
                  :before-until #'md-roam-preview-get-contents)
      ;; For `before-save-hook'
      (advice-add #'org-roam--replace-roam-links-on-save-h
                  :before-until #'md-roam--replace-roam-links-on-save-h)
      ;; For `org-roam-buffer-p'
      (advice-add #'org-roam-buffer-p :before-until #'md-roam-buffer-p)
      ;; Avoid invalid-regexp in `org-roam-node-open'
      (advice-add #'org-show-context :before-until #'md-roam-do-not-show-context)
      ;; Insert wiki-link when inserting a new note with using `org-roam-insert'
      (advice-add #'org-roam-capture--finalize-insert-link
                  :before-until #'md-roam-capture--finalize-insert-link)
      ;; Completion-at-point
      ;; Append to the back of the functions list so that md-roam's one get called
      ;; before org-roam ones (org-roam dolist, resulting in reversing the order)
      (add-to-list 'org-roam-completion-functions
                   #'md-roam-complete-wiki-link-at-point 'append)
      (add-to-list 'org-roam-completion-functions
                   #'md-roam-complete-everywhere 'append)))
   (t
    ;; Deactivate
    (advice-remove #'org-roam-db-update-file #'md-roam-db-update-file)
    (advice-remove #'org-roam-node-insert #'md-roam-node-insert)
    (advice-remove #'markdown-follow-wiki-link #'md-roam-follow-wiki-link)
    (remove-hook 'org-roam-capture-preface-hook #'md-roam-capture-preface)
    (advice-remove #'org-id-get #'md-roam-id-get)
    (advice-remove #'org-roam-id-at-point #'md-roam-id-at-point)
    (advice-remove #'org-roam-node-at-point #'md-roam-node-at-point)
    (advice-remove #'org-roam-preview-get-contents
                   #'md-roam-preview-get-contents)
    (advice-remove #'org-roam--replace-roam-links-on-save-h
                   #'md-roam--replace-roam-links-on-save-h)
    (advice-remove #'org-roam-buffer-p #'md-roam-buffer-p)
    (advice-remove #'org-show-context #'md-roam-do-not-show-context)
    (advice-remove #'org-roam-capture--finalize-insert-link
                   #'md-roam-capture--finalize-insert-link)
    (remove-hook 'org-roam-completion-functions
                 #'md-roam-complete-wiki-link-at-point)
    (remove-hook 'org-roam-completion-functions
                 #'md-roam-complete-everywhere))))

;;;; Functions

;;; File utilities
;;; Macros seem to need to be defined before functions that use them
(defmacro md-roam-with-file (file keep-buf-p &rest body)
  "Execute BODY within FILE for Md-roam.
If FILE is nil, execute BODY in the current buffer.
Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
  (declare (indent 2) (debug t))
  `(let* (new-buf
          (auto-mode-alist nil)
          (find-file-hook nil)
          (buf (or (and (not ,file)
                        (current-buffer)) ;If FILE is nil, use current buffer
                   (find-buffer-visiting ,file) ; If FILE is already visited, find buffer
                   (progn
                     (setq new-buf t)
                     (find-file-noselect ,file)))) ; Else, visit FILE and return buffer
          res)
     (with-current-buffer buf
       (unless (equal major-mode 'markdown-mode)
         ;; Don't delay mode hooks
         ;; not done again.
         (markdown-mode))
       (setq res (progn ,@body))
       (unless (and new-buf (not ,keep-buf-p))
         (save-buffer)))
     (if (and new-buf (not ,keep-buf-p))
         (when (find-buffer-visiting ,file)
           (kill-buffer (find-buffer-visiting ,file))))
     res))

;;;;; Private
;;    None of the functions in Md-roam are meant to be interactive commands.
;;    This is because they are meant to extend Org-roam functions (mostly in
;;    `org-roam-db') by means of advice.  This means that you as a user don't
;;    have to thinkg about the difference between Org-roam and Md-roam.  You can
;;    just use the same Org-roam commands such as `org-roam-node-insert' and
;;    `org-roam-node-find' within markdown files.  The switch of context is
;;    detected by the file extension -- e.g. .md vs .org -- and Md-roam will
;;    take care of the difference of the context.

;;------------------------------------------------------------------------------
;;;;; DB related functions for `org-roam-db'

(defun md-roam-db-update-file (&optional file-path _no-require)
  "Update Org-roam cache for FILE-PATH.
This function is meant to be used as advising function for
`org-roam-db-update-file.'"
  (when (md-roam--markdown-file-p (or file-path (buffer-file-name (buffer-base-buffer))))
    (md-roam-with-file file-path nil
        (setq file-path (or file-path (buffer-file-name (buffer-base-buffer))))
        (let ((content-hash (org-roam-db--file-hash file-path))
              (db-hash (caar (org-roam-db-query [:select hash :from files
                                                         :where (= file $s1)] file-path))))
          (unless (string= content-hash db-hash)
            (md-roam-db-do-update))
          ;; For before-until advice
          t))))

(defun md-roam-db-do-update ()
  "Update db cache without checking if the file has been changed.
Requied for wiki link capture."
  (emacsql-with-transaction (org-roam-db)
    (save-excursion
      (org-roam-db-clear-file)
      (md-roam-db-insert-file)
      (md-roam-db-insert-file-node)
      (md-roam-db-insert-wiki-links)
      (md-roam-db-insert-citations)
      (md-roam-db-insert-links))))

(defun md-roam-db-insert-file (&optional hash)
    "Update the files table for the current buffer.
If UPDATE-P is non-nil, first remove the file in the database.
If HASH is non-nil, use that as the file's hash without recalculating it."
    (let* ((file (buffer-file-name))
           (file-title (or (md-roam-get-title) (file-name-base file)))
           (attr (file-attributes file))
           (atime (file-attribute-access-time attr))
           (mtime (file-attribute-modification-time attr))
           (hash (or hash (org-roam-db--file-hash file))))
      (org-roam-db-query
       [:insert :into files
                :values $v1]
       (list (vector file file-title hash atime mtime)))))

(defun md-roam-db-insert-file-node ()
  "Insert the file-level node into the Org-roam cache."
  ;; `org-roam-db-update-file' turns the mode to org-mode (in `org-roam-with-file' macro)
  ;; `markdown-mode' needs to be explicitly turned back on.
  ;; (markdown-mode)
  ;; Run org-roam hooks to re-set after-save-hooks, etc.
  (run-hooks 'org-roam-find-file-hook)
  ;; `org-with-point-at' macro does not seem to assume the buffer is Org
  (org-with-point-at 1
    (when-let ((id (md-roam-get-id)))
      (let* ((file (buffer-file-name (buffer-base-buffer)))
             (title (or (md-roam-get-title)
                        (file-relative-name file org-roam-directory)))
             (pos (point))
             (todo nil)
             (priority nil)
             (scheduled nil)
             (deadline nil)
             (level 0)
             (tags (md-roam-get-tags))
             ;; Properties are required for `org-roam-ui'
             ;; TODO other properties in frontmatter?
             (properties (list (cons "TITLE" title) (cons "ID" id)))
             (olp nil))
        (org-roam-db-query!
         (lambda (err)
           (lwarn 'org-roam :warning "%s for %s (%s) in %s"
                  (error-message-string err)
                  title id file))
         [:insert :into nodes
                  :values $v1]
         (vector id file level pos todo priority
                 scheduled deadline title properties olp))
        (when tags
          (org-roam-db-query
           [:insert :into tags
                    :values $v1]
           (mapcar (lambda (tag)
                     (vector id (substring-no-properties tag)))
                   tags)))
        (md-roam-db-insert-aliases)
        (md-roam-db-insert-refs)))))

(defun md-roam-db-insert-wiki-links ()
  "Insert Markdown wiki links in current buffer into Org-roam cache."
  (org-with-point-at (md-roam-get-yaml-front-matter-endpoint)
    (let ((type "id")
          (source (md-roam-get-id))
          (properties (list :outline nil)))
      (when source
        (while (re-search-forward "\\[\\[\\([^]]+\\)\\]\\]" nil t)
          (let* ((name (match-string-no-properties 1))
                 (node (or (org-roam-node-from-title-or-alias name)
                           (org-roam-node-from-title-or-alias (replace-regexp-in-string "[\n ]+" " " name))
                           (org-roam-node-create :id name)))
                 (path (org-roam-node-id node)))
            ;; insert to cache the link only there is a file for the
            ;; destination node
            (when (org-roam-node-file (org-roam-populate node))
              (org-roam-db-query
               [:insert :into links
                        :values $v1]
               (vector (point) source path type properties)))))))))

(defun md-roam-db-insert-links ()
  "Insert URL and file links in current buffer into Org-roam cache.
URLs are for refs.  File links are for backlinks if the target
files are in `org-roam-directory'."
  (org-with-point-at (md-roam-get-yaml-front-matter-endpoint)
    (let  ((source (md-roam-get-id))
           (properties (list :outline nil)))
      (while (re-search-forward md-roam-regex-link-inline nil t)
        (unless (string-empty-p (match-string-no-properties 6)) ;; fix #73
          (let* ((url (match-string-no-properties 6))
                 (parsed-url (url-generic-parse-url url))
                 ;; If there url-type is nil then it can be a file link.
                 ;; File links require tye type to be id for Org-roam
                 (type (or (url-type parsed-url) "id"))
                 (file-path (when (and (string-equal type "id")
                                       ;; Avoid inserting the link to DB if it's not `md-roam-file-extension'
                                       (md-roam--markdown-file-p (url-filename parsed-url)))
                              ;; file-path, if exists, needs to be an absolute
                              ;; path as that's what Org-roam stores in the cache.
                              (buffer-file-name (find-file-noselect (url-filename parsed-url) 'NOWARN))))
                 ;; If file-path is non-nil, check Org-roam db if it is
                 ;; in Org-roam cache. Set ID to path.  If file-path is
                 ;; nil, get URL for refs.

                 ;; TODO Need refactoring. path is set to nil when
                 ;; file-path is nil (when a file is not
                 ;; a md roam file).  The behaviour is correct,
                 ;; but it's not explicit.
                 (path (if file-path (md-roam-db-id-from-file-path file-path)
                         ;; If file-path is nil, then
                         (when (string-match org-link-plain-re url)
                           (match-string-no-properties 2 url)))))
            (when (and type source path)
              (org-roam-db-query
               [:insert :into links
                        :values $v1]
               (vector (point) source path type properties)))))))))

(defun md-roam-db-insert-citations ()
  "Insert data for citations in the current buffer into Org-roam cache.
The citation is defined in Pandoc syntax such as
\"[@citation-key]\"."
  (org-with-point-at (md-roam-get-yaml-front-matter-endpoint)
    (let ((source (md-roam-get-id))
          ;; TODO outline path always nil
          (properties (list :outline nil)))
      (when source
        (while (re-search-forward md-roam-regex-in-text-citation-2 nil t)
          (when-let
              ;; remove "@" for key
              ((key (match-string-no-properties 2)))
            (org-roam-db-query
             [:insert :into citations
                      :values $v1]
             (vector source key (match-beginning 2) properties))))))))

(defun md-roam-db-insert-aliases ()
  "Insert aliases in current buffer into Org-roam cache.
The aliases must be defined witin the frontmatter.

Aliases must be defined within square brakets:
    [\"alias1\", \"alias of this note\"]

TODO: Other formats?"
  (when-let* ((node-id (md-roam-get-id))
              (frontmatter (md-roam-get-yaml-front-matter))
              (aliases (and frontmatter
                            (string-match md-roam-regex-aliases frontmatter)
                            (md-roam--yaml-seq-to-list
                             (match-string-no-properties 2 frontmatter)))))
    (org-roam-db-query [:insert :into aliases
                                :values $v1]
                       (mapcar (lambda (alias)
                                 (vector node-id alias))
                               aliases))))

(defun md-roam-db-insert-refs ()
  "Insert refs in current buffer into Org-roam cache.
The refs must be defined witin the frontmatter.

TODO other formats?"
  (when-let* ((node-id (md-roam-get-id))
              (frontmatter (md-roam-get-yaml-front-matter))
              (refs (and frontmatter
                         (string-match md-roam-regex-ref-keys frontmatter)
                         (split-string-and-unquote
                          (match-string-no-properties 2 frontmatter)))))
    (let (rows)
      (dolist (ref refs)
        (save-match-data
          (cond ((string-match org-link-plain-re ref)
                 (push (vector node-id (match-string 2 ref) (match-string 1 ref)) rows))
                (t
                 (push (vector node-id ref "cite") rows)))))
      (when rows
        (org-roam-db-query [:insert :into refs
                            :values $v1]
                           rows)))))

(defun md-roam-db-id-from-file-path (file-path)
  "Return node ID from FILE-PATH.
FILE-PATH must be an absolute path to the file in question."
  (when-let ((path (when (file-name-absolute-p file-path) file-path)))
    (caar (org-roam-db-query [:select [id] :from nodes
                              :where (= file $s1)]
                             path))))

(defun md-roam-db-file-relative-path-from-id (id)
  "Return file relative path from ID."
  (file-relative-name
   (caar (org-roam-db-query [:select [file] :from nodes
                                     :where (= id $s1)]
                            id))))

;;------------------------------------------------------------------------------
;;;;; Functions for other commands: node-insert and follow-wiki-link

(cl-defun md-roam-node-insert (&optional filter-fn &key templates info)
  "Find an Org-roam node and insert (where the point is) an \"id:\" link to it.
FILTER-FN is a function to filter out nodes: it takes an `org-roam-node',
and when nil is returned the node will be filtered out.
The TEMPLATES, if provided, override the list of capture templates (see
`org-roam-capture-'.)
The INFO, if provided, is passed to the underlying `org-roam-capture-'."
  (when (md-roam--markdown-file-p (buffer-file-name (buffer-base-buffer)))
    (unwind-protect
        ;; Group functions together to avoid inconsistent state on quit
        (atomic-change-group
          (let* (region-text
                 beg end
                 (_ (when (region-active-p)
                      (setq beg (set-marker (make-marker) (region-beginning)))
                      (setq end (set-marker (make-marker) (region-end)))
                      (setq region-text (org-link-display-format (buffer-substring-no-properties beg end)))))
                 (node (org-roam-node-read region-text filter-fn))
                 (description (or region-text
                                  (org-roam-node-formatted node))))
            (if (org-roam-node-id node)
                (progn
                  (when region-text
                    (delete-region beg end)
                    (set-marker beg nil)
                    (set-marker end nil))
                  (insert (md-roam--wiki-link-create (org-roam-node-id node)
                                                     description
                                                     (org-roam-node-title node)))
                  ;; for advice
                  t)
              (org-roam-capture-
               :node node
               :info info
               :templates templates
               :props (append
                       (when (and beg end)
                         (list :region (cons beg end)))
                       (list :insert-at (point-marker)
                             :link-description description
                             :finalize 'insert-link)))
              ;; for advice
              t)))
      (deactivate-mark)
      ;; for advice
      t)))

(defun md-roam-capture--finalize-insert-link ()
  "Insert a wiki-link to ID when `org-roam-insert' for a new note.
This is md-roam equivalent of `org-roam-capture--finalize-insert-link'."
  (when (md-roam--markdown-file-p (buffer-file-name (buffer-base-buffer)))
    (when-let* ((mkr (org-roam-capture--get :call-location))
                (buf (marker-buffer mkr)))
      (with-current-buffer buf
        (when-let ((region (org-roam-capture--get :region)))
          (org-roam-unshield-region (car region) (cdr region))
          (delete-region (car region) (cdr region))
          (set-marker (car region) nil)
          (set-marker (cdr region) nil))
        (let* ((id (org-roam-capture--get :id))
               (description (org-roam-capture--get :link-description))
               (link (md-roam--wiki-link-create id description description)))
          (if (eq (point) (marker-position mkr))
              (insert link)
            (org-with-point-at mkr
              (insert link)))
          (run-hook-with-args 'org-roam-post-node-insert-hook
                              id
                              description))))
    ;; for advice
    t))

(defun md-roam-follow-wiki-link (name &optional other)
  "Follow wiki link NAME if there is the linked file exists.
If the linked NAME does not yet exist, call `org-roam-find-node'
to capture a new file with using the text as the title.

It is meant to advice `markdown-follow-wiki-link'.

When OTHER is non-nil by using prefix argument, open the file in
another window.  This is not relevant if file does not exist."
  (when (org-roam-file-p (buffer-file-name (buffer-base-buffer)))
    (if-let* ((node (or (org-roam-node-from-title-or-alias name)
                        (org-roam-node-create :id name)))
              (node-populated (org-roam-populate node))
              (file (org-roam-node-file node-populated)))
        (when file
          (if other (find-file-other-window file) (find-file file)))
      (message (format "No Org-roam node found for \"%s\"" name))
      ;; TODO the source file needs to be saved again to update link for the
      ;; backlink to be cached.  This should be in the capture finaliztion
      ;; procss after the new buffer is saved (aborted should not be saved)
      (org-roam-capture-
       :node (org-roam-node-create :title name)
       :props '(:finalize md-roam-find-file)))
    t))

;; Capture needs to update the cache when wikilink does not have a target file.
(defun md-roam-find-file ()
  "Used in`md-roam-follow-wiki-link'.
When the wiki link target file does not yet exist, Md-roam
prompts for a new file with Org-roam captuure process.  When
finalizing the capture process, it updates the Org-roam cache for
the source file to cache the link from source to target."
  (let ((new-file (org-roam-capture--get :new-file)))
    (unless org-note-abort
      (when-let ((original-buf (org-capture-get :original-buffer)))
        (with-current-buffer original-buf
          (md-roam-db-do-update))
        (find-file new-file)))))

(defun md-roam-do-not-show-context (&optional _key)
  "Used in `org-roam-node-open' to avoid error.
invalid-regexp \"Invalid regular expression\"."
  (when (md-roam--markdown-file-p (buffer-file-name (buffer-base-buffer)))
    t))

;;------------------------------------------------------------------------------
;;;;; Functions for `org-roam-capture'

(defun md-roam-id-get (&rest _args)
  "This is meant to replace `org-id-get' for markdown buffers.
`org-roam-capture' process tries to create and add ID in the
Org's property drawer for a new file is being created.  For
markdown files, this should be prevented.  We can achieve this
because currently this function does not implement the create
process \(for _create argument\).

TODO CREATE process to insert a new ID within frontmatter."
  (when (md-roam--markdown-file-p (buffer-file-name (buffer-base-buffer)))
    (md-roam-get-id)))

(defun md-roam-id-at-point ()
  "Return the ID at point, if any.
This function is a wrapper for `md-roam-id-get'. For md-roam, the
ID is always at the file level; headline node exits."
  (when (md-roam--markdown-file-p (buffer-file-name (buffer-base-buffer)))
    (md-roam-id-get)))

(defun md-roam-capture-preface ()
  "."
  (advice-add #'org-entry-put :before-until #'md-roam-entry-put)
  (add-hook 'org-capture-after-finalize-hook #'md-roam-capture-after-finalize)
  ;; Need to retrun nil for `org-roam-capture--prepare-buffer' to run the normal
  ;; process.
  nil)

(defun md-roam-entry-put (_pom _property _value)
  "Return t and do nothing when current buffer visiting markdown file.
Only for `md-roam'."
  (when (md-roam--markdown-file-p (buffer-file-name (buffer-base-buffer)))
    t))

(defun md-roam-capture-after-finalize ()
  "Remove the advice from `org-entry-put'."
  (advice-remove #'org-entry-put #'md-roam-entry-put)
  (remove-hook 'org-capture-after-finalize-hook #'md-roam-capture-after-finalize))

;;------------------------------------------------------------------------------
;;;;; Functions for `org-roam-buffer'

(defun md-roam-node-at-point (&optional _assert)
  "Return the node at point.
If ASSERT, throw an error."
  (when (and (buffer-file-name (buffer-base-buffer))
             (md-roam--markdown-file-p (buffer-file-name (buffer-base-buffer))))
    (org-roam-populate (org-roam-node-create :id (md-roam-get-id)))))

(defun md-roam-preview-get-contents (file pt)
  "Get preview content for FILE at PT."
  (when (md-roam--markdown-file-p file)
    (save-excursion
      (org-roam-with-temp-buffer file
        (org-with-wide-buffer
         (goto-char pt)
         (let ((beg (progn (markdown-backward-paragraph)
                           (point)))
               (end (progn (markdown-forward-paragraph)
                           (point))))
           (string-trim (buffer-substring-no-properties beg end))))))))

;;------------------------------------------------------------------------------
;;;;; Get functions, mainly for properties in frontmatter

(defun md-roam-get-yaml-front-matter ()
  "Return the text of the YAML front matter of the current buffer.
Return nil if the front matter does not exist, or incorrectly delineated by
'---'.  The front matter is required to be at the beginning of the file."

  (save-excursion
    (goto-char (point-min))
    (when-let
        ((startpoint (re-search-forward
                      md-roam-regex-yaml-font-matter-beginning 4 t 1))
         ;; The beginning needs to be in the beginning of buffer
         (endpoint (re-search-forward
                    md-roam-regex-yaml-font-matter-ending nil t 1)))
      (buffer-substring-no-properties startpoint endpoint))))

(defun md-roam-get-yaml-front-matter-endpoint ()
  "Return the endpoint of the YAML front matter of the current buffer.
Return nil if the front matter does not exist, or incorrectly delineated by
'---'.  The front matter is required to be at the beginning of the file."

  (save-excursion
    (goto-char (point-min))
    (when-let
        ((startpoint (re-search-forward
                      md-roam-regex-yaml-font-matter-beginning 4 t 1))
         ;; The beginning needs to be in the beginning of buffer
         (endpoint (re-search-forward
                    md-roam-regex-yaml-font-matter-ending nil t 1)))
      endpoint)))

(defun md-roam-get-tags ()
  "Get tags defined in the Zettlr style within frontmatter."
  (let ((endpoint (md-roam-get-yaml-front-matter-endpoint)))
    (cond (endpoint
           (save-excursion
             (let (tags)
               (goto-char (point-min))
               (while (re-search-forward md-roam-regex-tags-zettlr-style endpoint t)
                 (let ((tag (match-string-no-properties 2)))
                   (when tag
                     (setq tags
                           (append tags
                                   ;; Remove the first char @ or #
                                   (list (if (eql 0 (string-match "[@#]" tag))
                                             (substring tag 1)
                                           tag)))))))
               tags))))))

(defun md-roam-get-title ()
  "Extract title from the current buffer (markdown file with YAML frontmatter).

This function looks for the YAML frontmatter delineator '---' begining of
the buffer.  No space is allowed before or after the delineator.

It assumes:
 (1) Current buffer is a markdonw file (but does not check it)
 (2) It has title in the YAML frontmatter on top of the file
 (3) The format is 'title: The Document Title'"

  (let ((frontmatter (md-roam-get-yaml-front-matter)))
    (when (and frontmatter
               (string-match md-roam-regex-title frontmatter))
      (match-string-no-properties 2 frontmatter))))

(defun md-roam-get-id ()
  "Extract id from the current buffer (markdown file with YAML frontmatter).

This function looks for the YAML frontmatter delineator '---' begining of
the buffer.  No space is allowed before or after the delineator.

It assumes:
 (1) Current buffer is a markdonw file (but does not check it)
 (2) It has title in the YAML frontmatter on top of the file
 (3) The format is 'id: <string>'"

  (let ((frontmatter (md-roam-get-yaml-front-matter)))
    (when (and frontmatter
               (string-match md-roam-regex-id frontmatter))
      (match-string-no-properties 2 frontmatter))))

;;------------------------------------------------------------------------------
;;;;; Completion at point

(defun md-roam-complete-wiki-link-at-point ()
  "Complete wiki link at point to an existing Org-roam node.
It puts the title, not IDs."
  (when (md-roam--markdown-file-p (buffer-file-name (buffer-base-buffer)))
    (let (start end)
      (when (org-in-regexp org-roam-bracket-completion-re 1)
        (setq start (match-beginning 2)
              end (match-end 2))
        (list start end
              (org-roam--get-titles)
              :exit-function
              (lambda (&rest _)
                (forward-char 2)))))))

(defun md-roam-complete-everywhere ()
  "Complete symbol at point as a link completion to an Org-roam node.
This is a `completion-at-point' function, and is active when
`org-roam-completion-everywhere' is non-nil.

Unlike `org-roam-complete-link-at-point' this will complete even
outside of the bracket syntax for wiki links (i.e. \"[[|]]\"),
hence \"everywhere\"."
  (when (and (md-roam--markdown-file-p (buffer-file-name (buffer-base-buffer)))
             org-roam-completion-everywhere
             (thing-at-point 'word)
             (not (save-match-data (org-in-regexp org-link-any-re))))
    (let ((bounds (bounds-of-thing-at-point 'word)))
      (list (car bounds) (cdr bounds)
            (org-roam--get-titles)
            :exit-function
            (lambda (str _status)
              (delete-char (- (length str)))
              (insert "[[" str "]]"))
            ;; Proceed with the next completion function if the returned titles
            ;; do not match. This allows the default Org capfs or custom capfs
            ;; of lower priority to run.
            :exclusive 'no))))

;;------------------------------------------------------------------------------
;;;;; Replace roam links
;;    Relavant for the [[roam:]] and [[wiki link]] form

(defun md-roam--replace-roam-links-on-save-h ()
  "Avoid running `org-roam-link-replace-all' on `before-save-hook'.
It's set by `org-roam-find-file-hook' and can cause an issue for
Md-roam files."
  (when (md-roam--markdown-file-p (buffer-file-name (buffer-base-buffer)))
    ;; do nothing for now and return t for advice
    t))

;;------------------------------------------------------------------------------
;;;;; `md-roam-buffer-p' for `org-roam-buffer-list'

(defun md-roam-buffer-p (&optional buffer)
  "Return t if BUFFER is for an Md-roam file.
If BUFFER is not specified, use the current buffer."
  (let ((buffer (or buffer (current-buffer))))
    (with-current-buffer buffer
      (md-roam--markdown-file-p (buffer-file-name (buffer-base-buffer))))))

;;------------------------------------------------------------------------------
;;;;; Utility functions

;;;TODO This file can be unit tested
(defun md-roam--markdown-file-p (file)
  "Return non-nil if FILE is pointing to a markdown file.
`md-roam-file-extension' can be either a string or a list of strings.
Return nil if not."
  (when file
    (let ((ext (org-roam--file-name-extension file)))
      (if (stringp md-roam-file-extension)
          (string-equal ext md-roam-file-extension)
        ;; If not string, it must be a list of string
        (member ext md-roam-file-extension)))))

(defun md-roam--remove-single-quotes (str)
  "Check if STR is surrounded by single-quotes, and remove them.
If not, return STR as is."
  (let ((regexp "\\('\\)\\(.*\\)\\('\\)"))
    (if (string-match regexp str)
        (match-string-no-properties 2 str)
      str)))

(defun md-roam--yaml-seq-to-list (seq)
  "Return a list from YAML SEQ formatted in the flow style.
SEQ = sequence, It's an array.  At the moment, only the flow
style works.

See the spec at https://yaml.org/spec/1.2/spec.html Flow style:

    !!seq [ Clark Evans, Ingy döt Net, Oren Ben-Kiki ].

The items in the sequence (array) can be separated by different ways.

    1. Spaces like the example from the spec above
    2. Single-quotes 'item'
    3. Double-quotes \"item\"

Do not escape the singe- or double-quotations. At the moment,
that doeslead to error.

The regexp is meant to to match YAML sequence formatted in the
flow style.  At the moment, only the flow style is
considered. The number of spaces between the squeare bracket and
the first/last item should not matter.

    [item1, item2, item3]
    [ item1, item2, item3 ]

These should be equally valid."

  (let ((regexp "\\(\\[\s*\\)\\(.*\\)\\(\s*\\]\\)")
        (separator ",\s*"))
    (when (string-match regexp seq)
      (let ((items (split-string-and-unquote
                    (match-string-no-properties 2 seq) separator)))
        (mapcar #'md-roam--remove-single-quotes items)))))

(defun md-roam--yaml-split-seq (seq)
  "."
  (let ((regexp "\\(\s*\\)\\(.*\\)\\(\s*\\)")
        (separator ",\s*"))
    (when (string-match regexp seq)
      (let ((items (split-string-and-unquote
                    (match-string-no-properties 2 seq) separator)))
        (mapcar #'md-roam--remove-single-quotes items)))))

(defun md-roam--wiki-link-create (id description title)
  "Return wiki-link string.
This function uses `md-roam-node-insert-type' to return the
approapriate wiki-link.

ID is the node ID.  DESCRIPTION is description used in
`org-roam-insert'.  TITLE is the title, alias, or description of
the node being inserted."

    (concat "[["
            (cond
             ((eq md-roam-node-insert-type 'id)
              (concat id "]] " description))
             ((eq md-roam-node-insert-type 'title-or-alias)
              (concat title "]]")))))

(provide 'md-roam)
;;; md-roam.el ends here