;; Modern Org-mode styling
(use-package org-modern
  :hook
  (org-mode . org-modern-mode)
  (org-agenda-finalize . org-modern-agenda)
  :custom
  ;; Heading styles
  (org-modern-star 'replace)
  (org-modern-hide-stars t)
  (org-modern-table t)
  (org-modern-table-vertical 1)
  (org-modern-table-horizontal 0.2)

  ;; List bullets
  (org-modern-list '((43 . "➤")   ; +
                     (45 . "–")   ; -
                     (42 . "•"))) ; *

  ;; Block delimiters
  (org-modern-block-name '(("src" "»" "«")
                           ("example" "»–" "–«")
                           ("quote" "❝" "❞")
                           ("export" "⏩" "⏪")))

  ;; Keywords styling
  (org-modern-keyword t)
  (org-modern-checkbox nil)
  (org-modern-horizontal-rule t)

  ;; Timestamps
  (org-modern-timestamp t)
  (org-modern-statistics t)

  ;; Tags
  (org-modern-tag t)
  (org-modern-priority t)

  ;; Todo keywords
  (org-modern-todo t)
  (org-modern-todo-faces
   '(("TODO" :background "#ff6c6b" :foreground "#282c34" :weight bold)
     ("DOING" :background "#51afef" :foreground "#282c34" :weight bold)
     ("REVIEW" :background "#ecbe7b" :foreground "#282c34" :weight bold)
     ("DONE" :background "#98be65" :foreground "#282c34" :weight bold)
     ("CANCEL" :background "#5B6268" :foreground "#282c34" :weight bold))))

(use-package org-roam
  :after org
  :demand t
  :init
  ;; Ensure org-roam directory exists before package loads
  (let ((roam-dir (file-truename "~/org-roam/")))
    (unless (file-directory-p roam-dir)
      (make-directory roam-dir t)))
  :custom
  ;; Directory where all your notes will be stored
  (org-roam-directory (file-truename "~/org-roam/"))

  ;; Better database location (avoid cluttering org-roam directory)
  (org-roam-db-location (expand-file-name "org-roam.db" user-emacs-directory))

  ;; Enable completion everywhere (for inserting links)
  (org-roam-completion-everywhere t)

  ;; Configure how nodes are displayed in completion
  (org-roam-node-display-template
   (concat "${title:*} " (propertize "${tags:10}" 'face 'org-tag)))

  :bind
  (("C-c n l" . org-roam-buffer-toggle)         ;; Show backlinks sidebar
   ("C-c n f" . org-roam-node-find)             ;; Find or create a note
   ("C-c n i" . org-roam-node-insert)           ;; Insert a link to a note
   ("C-c n c" . org-roam-capture)               ;; Quick capture
   ("C-c n j" . org-roam-dailies-capture-today) ;; Daily note
   ("C-c n g" . org-roam-graph)                 ;; Visualize the graph
   :map org-mode-map
   ("C-M-i"   . completion-at-point))           ;; Complete link at point

  :config
  ;; Initialize org-roam database and sync on startup
  (org-roam-db-autosync-mode 1))

(use-package org-roam
  :custom
  ;; Capture templates for different note types
  (org-roam-capture-templates
   '(("d" "default" plain
      "%?"
      :target (file+head "%<%Y%m%dT%H%M%S>--${slug}.org"
                         "#+title: ${title}\n#+date: %U\n#+filetags: \n\n")
      :unnarrowed t)

     ("p" "permanent" plain
      "* Source\n\n%?\n\n* Content\n\n\n* Links\n"
      :target (file+head "permanent/%<%Y%m%dT%H%M%S>--${slug}.org"
                         "#+title: ${title}\n#+date: %U\n#+filetags: :permanent:\n\n")
      :unnarrowed t)

     ("l" "literature" plain
      "* Source\n\nAuthor: %^{Author}\nTitle: ${title}\nYear: %^{Year}\n\n%?\n\n* Summary\n\n\n* Key Points\n\n\n* Quotes\n\n\n* Related\n"
      :target (file+head "literature/%<%Y%m%dT%H%M%S>--${slug}.org"
                         "#+title: ${title}\n#+date: %U\n#+filetags: :literature:\n\n")
      :unnarrowed t)

     ("c" "concept" plain
      "* Definition\n\n%?\n\n* Examples\n\n\n* Related Concepts\n"
      :target (file+head "concepts/%<%Y%m%dT%H%M%S>--${slug}.org"
                         "#+title: ${title}\n#+date: %U\n#+filetags: :concept:\n\n")
      :unnarrowed t)

     ("r" "reference" plain
      "* %?\n"
      :target (file+head "reference/%<%Y%m%dT%H%M%S>--${slug}.org"
                         "#+title: ${title}\n#+date: %U\n#+filetags: :reference:\n\n")
      :unnarrowed t))))

(use-package org-roam
  :custom
  ;; Store daily notes in a dedicated subdirectory
  (org-roam-dailies-directory "daily/")

  ;; Capture templates for daily notes
  (org-roam-dailies-capture-templates
   '(("d" "default" entry
      "* %?"
      :target (file+head "%<%Y-%m-%d>.org"
                         "#+title: %<%Y-%m-%d (%A)>\n#+filetags: :daily:\n\n"))

     ("m" "meeting" entry
      "* %<%H:%M> Meeting: %^{Meeting Title}\n\n** Attendees\n%?\n\n** Notes\n\n\n** Action Items\n"
      :target (file+head "%<%Y-%m-%d>.org"
                         "#+title: %<%Y-%m-%d (%A)>\n#+filetags: :daily:\n\n"))

     ("j" "journal" entry
      "* %<%H:%M> Journal\n\n%?"
      :target (file+head "%<%Y-%m-%d>.org"
                         "#+title: %<%Y-%m-%d (%A)>\n#+filetags: :daily:journal:\n\n"))

     ("t" "task" entry
      "* TODO %?\n  SCHEDULED: %t\n"
      :target (file+head "%<%Y-%m-%d>.org"
                         "#+title: %<%Y-%m-%d (%A)>\n#+filetags: :daily:\n\n"))))

  :bind
  (("C-c n t" . org-roam-dailies-goto-today)
   ("C-c n y" . org-roam-dailies-goto-yesterday)
   ("C-c n d" . org-roam-dailies-goto-date)
   ("C-c n n" . org-roam-dailies-goto-next-note)
   ("C-c n p" . org-roam-dailies-goto-previous-note)))

(use-package org-roam
  :config
  ;; Custom function to display nodes with more context
  (setq org-roam-node-display-template
        (concat "${type:15} ${title:*} " (propertize "${tags:20}" 'face 'org-tag)))

  ;; Add custom properties to node display
  (cl-defmethod org-roam-node-type ((node org-roam-node))
    "Return the TYPE of NODE based on tags or directory."
    (let ((tags (org-roam-node-tags node))
          (file (org-roam-node-file node)))
      (cond
       ((member "permanent" tags) "📝 Permanent")
       ((member "literature" tags) "📚 Literature")
       ((member "concept" tags) "💡 Concept")
       ((member "reference" tags) "📖 Reference")
       ((member "daily" tags) "📅 Daily")
       ((string-match-p "/daily/" file) "📅 Daily")
       ((string-match-p "/literature/" file) "📚 Literature")
       ((string-match-p "/permanent/" file) "📝 Permanent")
       ((string-match-p "/concepts/" file) "💡 Concept")
       (t "📄 Note")))))

(use-package org-roam
  :custom
  ;; Graphviz executable for generating graphs
  (org-roam-graph-executable (executable-find "dot"))

  ;; Exclude certain tags from the graph for cleaner visualization
  ;; (org-roam-graph-exclude-matcher '("daily" "fleeting"))
  (org-roam-graph-exclude-matcher '())
  ;; Use specific program for graph generation
  (org-roam-graph-viewer (executable-find "open"))  ;; macOS
  ;; For Linux: (org-roam-graph-viewer "xdg-open")
  ;; For Windows: (org-roam-graph-viewer "start")

  ;; Additional graph settings
  (org-roam-graph-extra-config
   '(("overlap" . "false")
     ("splines" . "true")
     ("rankdir" . "LR"))))  ;; Left to Right layout

;; Skip org-roam-ui on server (requires browser/GUI)
(unless emacs-server-mode
  (use-package org-roam-ui
    :after org-roam
    :custom
    (org-roam-ui-sync-theme t)              ;; Sync with Emacs theme
    (org-roam-ui-follow t)                  ;; Follow current note in UI
    (org-roam-ui-update-on-save t)          ;; Update graph on save
    (org-roam-ui-open-on-start t)           ;; Open browser when activated
    (org-roam-ui-browser-function #'browse-url-default-browser)  ;; Use default browser
    :bind
    ("C-c n u" . org-roam-ui-mode)))

  (use-package org-roam
    :custom
    ;; Increase cache size for better performance
    (org-roam-db-gc-threshold most-positive-fixnum)

    ;; Update database asynchronously
    (org-roam-db-update-method 'immediate)

    :config
    ;; Auto-save database periodically
    (run-with-idle-timer 300 t #'org-roam-db-sync))

  ;; Helper function for safe note deletion
  (defun fu/org-roam-node-delete (&optional node)
    "Delete an org-roam NODE after showing backlinks warning.
If NODE is not provided, prompt to select a note from minibuffer.
If called from within a note, can use current note."
    (interactive)
    (let* ((node (or node
                     (if (derived-mode-p 'org-mode)
                         ;; Try current node first, fall back to selection
                         (or (org-roam-node-at-point)
                             (org-roam-node-read))
                       ;; Not in org-mode, always prompt
                       (org-roam-node-read))))
           (file (org-roam-node-file node))
           (title (org-roam-node-title node))
           (backlinks (org-roam-backlinks-get node))
           (buffer (find-buffer-visiting file)))
      (if backlinks
          (progn
            ;; Open the file if not already open
            (unless buffer
              (find-file file))
            (org-roam-buffer-toggle)
            (message "WARNING: %d notes link to '%s'! Check backlinks first."
                     (length backlinks) title))
        (when (yes-or-no-p (format "Delete '%s'? " title))
          (when buffer (kill-buffer buffer))
          (delete-file file)
          (org-roam-db-sync)
          (message "Note '%s' deleted and database synced." title)))))

  (provide 'org-conf)
  ;;; org-conf.el ends here

(use-package org-jira
  :after org
  :custom
  ;; Directory to store org-jira files
  (org-jira-working-dir (expand-file-name "jira/" org-directory))

  ;; Default JQL query for fetching issues
  (org-jira-default-jql
   "assignee = currentUser() AND resolution = Unresolved ORDER BY priority DESC, updated DESC")

  ;; How to handle issue priority in Org
  (org-jira-priority-to-org-priority-alist
   '(("Highest" . ?A)
     ("High"    . ?B)
     ("Medium"  . ?C)
     ("Low"     . ?D)
     ("Lowest"  . ?E)))

  ;; Map Jira status to Org TODO keywords
  (org-jira-jira-status-to-org-keyword-alist
   '(("To Do"       . "TODO")
     ("In Progress" . "DOING")
     ("In Review"   . "REVIEW")
     ("Done"        . "DONE")
     ("Closed"      . "DONE")))

  :config
  ;; Ensure jira working directory exists
  (unless (file-directory-p org-jira-working-dir)
    (make-directory org-jira-working-dir t))

  :bind
  (("C-c j g" . org-jira-get-issues)                      ;; Fetch issues with default JQL
   ("C-c j q" . org-jira-get-issues-from-custom-jql)      ;; Fetch from custom JQL
   ("C-c j c" . org-jira-create-issue)                    ;; Create a new issue
   ("C-c j u" . org-jira-update-issue)                    ;; Update current issue
   ("C-c j p" . org-jira-progress-issue)                  ;; Transition issue status
   ("C-c j a" . org-jira-assign-issue)                    ;; Assign issue to someone
   ("C-c j r" . org-jira-refresh-issue)                   ;; Refresh current issue
   ("C-c j w" . org-jira-update-worklogs-from-org-clocks) ;; Sync worklogs
   ("C-c j t" . org-jira-todo-to-jira)                    ;; Create Jira issue from TODO
   ("C-c j b" . org-jira-browse-issue)))                  ;; Open issue in browser

;; Custom JQL queries - add to your config
(setq org-jira-custom-jqls
      '(;; Current sprint issues
        (:jql "project = PROJ AND sprint in openSprints() ORDER BY rank"
         :filename "current-sprint")

        ;; My in-progress work
        (:jql "assignee = currentUser() AND status = 'In Progress' ORDER BY updated DESC"
         :filename "in-progress")

        ;; Issues I reported
        (:jql "reporter = currentUser() AND created >= -30d ORDER BY created DESC"
         :filename "my-reported")

        ;; High priority unresolved
        (:jql "assignee = currentUser() AND priority IN (Highest, High) AND resolution = Unresolved"
         :filename "high-priority")

        ;; Recently updated across team
        (:jql "project = PROJ AND updated >= -1d ORDER BY updated DESC"
         :filename "team-recent")))