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+;;; org-pdftools.el --- Support for links to documents in pdfview mode  -*- lexical-binding: t; -*-
+;; Copyright (C) 2020 Alexander Fu Xi
+
+;; Author: Alexander Fu Xi <fuxialexander@gmail.com>
+;; Maintainer: Alexander Fu Xi <fuxialexnader@gmail.com>
+;; Homepage: https://github.com/fuxialexander/org-pdftools
+;; Version: 1.0
+;; Keywords: convenience
+;; Package-Requires: ((emacs "26.1") (org "9.3.6") (pdf-tools "0.8") (org-noter "1.4.1"))
+
+;; 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:
+;; Add support for org links from pdftools buffers with more precise location control.
+;;
+;; https://github.com/fuxialexander/org-pdftools/
+
+
+;;; Code:
+(require 'subr-x)
+(require 'cl-lib)
+(require 'org)
+(require 'org-refile nil t)
+;; (require 'org-noter)
+(load-config "pdf.el")
+(require 'pdf-tools)
+(require 'pdf-view)
+(require 'pdf-annot)
+(require 'pdf-occur)
+
+(defgroup org-pdftools nil
+  "Tools for adding pdftools link support in Org mode."
+  :group 'tools)
+
+(defcustom org-pdftools-get-desc-function #'org-pdftools-get-desc-default
+  "A function that takes 3 arguments and output a link description.
+- `file': basename of the PDF file
+- `page': current page number converted to string
+- `text' (should have optional tag): additional text infomation like highlighted text or isearch string.
+See `org-pdftools-get-desc-default' as an example."
+
+  :group 'org-pdftools
+  :type 'function)
+(defcustom org-pdftools-path-generator #'abbreviate-file-name
+"Translate your PDF file path the way you like. Take buffer-file-name as the argument."
+  :group 'org-pdftools
+  :type 'function)
+(defcustom org-pdftools-path-resolver #'expand-file-name
+"Resolve your translated PDF file path back to an absolute path."
+  :group 'org-pdftools
+  :type 'function)
+(defcustom org-pdftools-open-custom-open nil
+  "Custom function to open linked pdf files."
+  :group 'org-pdftools
+  :type '(choice function nil))
+(defcustom org-pdftools-export-style 'pdftools
+  "Export style of org-pdftools links.
+- pdftools :: export the link as is
+- protocol :: export the link as a org-protocal link such that it could open pdf-tools when clicked
+"
+  :group 'org-pdftools
+  :type 'symbol)
+(defcustom org-pdftools-markup-pointer-function 'pdf-annot-add-underline-markup-annotation
+  "Color for markup pointer annotations.
+Can be one of highlight/underline/strikeout/squiggly."
+  :group 'org-pdftools
+  :type 'function)
+(defcustom org-pdftools-markup-pointer-color "#A9A9A9"
+  "Color for markup pointer annotations."
+  :group 'org-pdftools
+  :type 'string)
+(defcustom org-pdftools-markup-pointer-opacity 1.0
+  "Opacity for markup pointer annotations."
+  :group 'org-pdftools
+  :type 'float)
+(defcustom org-pdftools-free-pointer-icon "Circle"
+  "Color for free pointer annotations. Refer to `pdf-annot-standard-text-icons`."
+  :group 'org-pdftools
+  :type 'string)
+(defcustom org-pdftools-link-prefix "pdf"
+  "Prefix for org-pdftools link"
+  :group 'org-pdftools
+  :type 'string)
+(defcustom org-pdftools-search-string-separator "??"
+  "Separator of search-string."
+  :group 'org-pdftools
+  :type 'string)
+(defcustom org-pdftools-free-pointer-color "#FFFFFF"
+  "Color for free pointer annotations."
+  :group 'org-pdftools
+  :type 'string)
+(defcustom org-pdftools-free-pointer-opacity 1.0
+  "Opacity for free pointer annotations."
+  :group 'org-pdftools
+  :type 'float)
+
+
+;; pdf://path::page++height_percent;;annot_id??isearch_string or @@occur_search_string
+(defun org-pdftools-open-pdftools (link)
+  "Internal function to open org-pdftools LINK."
+  (let ((link-regexp
+         (concat "\\(.*\\)::\\([0-9]*\\)\\(\\+\\+\\)?\\([[0-9]\\.*[0-9]*\\)?\\(;;\\|"
+                 (regexp-quote org-pdftools-search-string-separator)
+                 "\\)?\\(.*\\)")))
+    (cond ((string-match link-regexp link)
+           (let ((path (match-string 1 link))
+                 (page (match-string 2 link))
+                 (height (match-string 4 link))
+                 annot-id
+                 search-string)
+             (cond ((string-equal
+                     (match-string 5 link)
+                     ";;")
+                    (setq annot-id
+                          (match-string 6 link)))
+                   ((string-equal
+                     (match-string 5 link)
+                     org-pdftools-search-string-separator)
+                    (setq search-string
+                          (replace-regexp-in-string
+                           "%20"
+                           " "
+                           (match-string 6 link)))))
+             (when (and path
+                        (not (string-empty-p path)))
+               (if (bound-and-true-p org-noter--session)
+                   (org-noter--with-valid-session
+                    (let ((doc (with-selected-window
+                                   (org-noter--get-doc-window)
+                                 buffer-file-name))
+                          (fullpath (funcall org-pdftools-path-resolver path)))
+                      (if (string-equal doc fullpath)
+                          (select-window
+                           (org-noter--get-doc-window))
+                        (let ((org-link-frame-setup
+                               (cl-acons 'file 'find-file-other-frame org-link-frame-setup)))
+                          (org-open-file fullpath 1)))))
+                 (org-open-file (funcall org-pdftools-path-resolver path) 1)))
+             (if (and page
+                      (not (string-empty-p page)))
+                 (progn
+                   (setq page (string-to-number page))
+                   (if (bound-and-true-p org-noter--session)
+                       (org-noter--with-valid-session
+                        (with-selected-window
+                            (org-noter--get-doc-window)
+                          (pdf-view-goto-page page)))
+                     (pdf-view-goto-page page)))
+               (setq page nil))
+             (when (and height
+                        (not (string-empty-p height)))
+               (if (bound-and-true-p org-noter--session)
+                   (org-noter--with-valid-session
+                    (with-selected-window
+                        (org-noter--get-doc-window)
+                      (image-set-window-vscroll
+                       (round
+                        (/
+                         (*
+                          (string-to-number height)
+                          (cdr (pdf-view-image-size)))
+                         (frame-char-height))))))
+                 (image-set-window-vscroll
+                  (round
+                   (/
+                    (*
+                     (string-to-number height)
+                     (cdr (pdf-view-image-size)))
+                    (frame-char-height))))))
+             (when (and annot-id
+                        (not (string-empty-p annot-id)))
+               (if (bound-and-true-p org-noter--session)
+                   (org-noter--with-valid-session
+                    (with-selected-window
+                        (org-noter--get-doc-window)
+                      (pdf-annot-show-annotation
+                       (pdf-info-getannot annot-id)
+                       t)))
+                 (pdf-annot-show-annotation
+                  (pdf-info-getannot annot-id)
+                  t)))
+             (when (and search-string
+                        (not (string-empty-p search-string)))
+               (if (bound-and-true-p org-noter--session)
+                   (org-noter--with-valid-session
+                    (with-selected-window
+                        (org-noter--get-doc-window)
+                      (isearch-mode t)
+                      (isearch-yank-string search-string)))
+                 (isearch-mode t)
+                 (isearch-yank-string search-string)))))
+          ((string-match
+            "\\(.*\\)@@\\(.*\\)"
+            link)
+           (let* ((paths (match-string 1 link))
+                  (occur-search-string (match-string 2 link))
+                  (pathlist (split-string paths "%&%")))
+             (pdf-occur-search
+              pathlist
+              occur-search-string)))
+          ((org-open-file link 1)))))
+
+(defun org-pdftools-get-link ()
+  "Get link from the active pdf buffer."
+  (let* ((path
+          (with-current-buffer (current-buffer)
+              (funcall org-pdftools-path-generator (buffer-file-name))))
+         (page (pdf-view-current-page))
+         (annot-id (if (pdf-view-active-region-p)
+                       (pdf-annot-get-id
+                        (funcall
+                         org-pdftools-markup-pointer-function
+                         (pdf-view-active-region t)
+                         org-pdftools-markup-pointer-color
+                         `((opacity . ,org-pdftools-markup-pointer-opacity))))
+                     (if (and (not (bound-and-true-p org-noter--session))
+                              (pdf-annot-getannots page))
+                         (condition-case nil
+                             (pdf-annot-get-id
+                              (pdf-annot-read-annotation
+                               "Click the annotation that you want to link to."))
+                           (error
+                            (if (y-or-n-p
+                                 "You can click anywhere on the page to add a link to. Do you want to do that? ")
+                                (pdf-annot-get-id
+                                 (funcall-interactively
+                                  #'pdf-annot-add-text-annotation
+                                  (pdf-util-read-image-position
+                                   "Click where a new text annotation should be added ...")
+                                  org-pdftools-free-pointer-icon
+                                  `((color . ,org-pdftools-free-pointer-color)
+                                    (opacity . ,org-pdftools-free-pointer-opacity))))
+                              nil)))
+                       (if (y-or-n-p
+                            "You can click anywhere on the page to add a link to. Do you want to do that? ")
+                           (pdf-annot-get-id
+                            (funcall-interactively
+                             #'pdf-annot-add-text-annotation
+                             (pdf-util-read-image-position
+                              "Click where a new text annotation should be added ...")
+                             org-pdftools-free-pointer-icon
+                             `((color . ,org-pdftools-free-pointer-color)
+                               (opacity . ,org-pdftools-free-pointer-opacity))))
+                         nil))))
+         (height (cond ((bound-and-true-p annot-id)
+                        (nth 1 (pdf-annot-get
+                                (pdf-info-getannot
+                                 annot-id
+                                 path)
+                                'edges)))
+                       (t
+                        (/
+                         (*
+                          (or (image-mode-window-get
+                               'vscroll)
+                              0)
+                          (frame-char-height))
+                         (float
+                          (cdr (pdf-view-image-size)))))))
+         ;; pdf://path::page++height_percent;;annot_id\\|??search-string
+         (search-string (if (and (not annot-id)
+                                 (y-or-n-p
+                                  "Do you want to add a isearch link? "))
+                            isearch-string
+                          ""))
+         (link (concat
+
+                org-pdftools-link-prefix ":"
+                path
+                "::"
+                (number-to-string page)
+                "++"
+                (format "%.2f" height)
+                (if annot-id
+                    (concat
+                     ";;"
+                     (symbol-name annot-id))
+                  (if (not (string-empty-p search-string))
+                      (concat
+                       org-pdftools-search-string-separator
+                       (replace-regexp-in-string
+                        " "
+                        "%20"
+                        search-string))
+                    (message
+                     "   Reminder: You haven't performed a isearch!") "")))))
+    link))
+
+(defun org-pdftools-get-desc-default (file page &optional text)
+  (concat file ".pdf: Page " page (when text (concat "; Quoting: " text))))
+
+;;;###autoload
+(defun org-pdftools-open (link)
+  "Function to open org-pdftools LINK."
+  (if (and (display-graphic-p)
+           (featurep 'pdf-tools))
+      (org-pdftools-open-pdftools
+       link)
+    (if (bound-and-true-p org-pdftools-open-custom-open)
+        (funcall org-pdftools-open-custom-open link)
+      (let* ((path (when (string-match
+                          "\\(.+\\)::.+" link)
+                     (match-string 1 link))))
+        (org-open-file path)))))
+
+;;;###autoload
+(defun org-pdftools-store-link ()
+  "Store a link to a pdfview/pdfoccur buffer."
+  (cond ((eq major-mode 'pdf-view-mode)
+         ;; This buffer is in pdf-view-mode
+         (let* ((file (file-name-base (pdf-view-buffer-file-name)))
+                (quot (if (pdf-view-active-region-p)
+                          (replace-regexp-in-string "\n" " "
+                                                    (mapconcat 'identity (pdf-view-active-region-text) ? ))))
+                (page (number-to-string (pdf-view-current-page)))
+                (link (org-pdftools-get-link))
+                (isearchstr (if (string-match (concat ".*" (regexp-quote org-pdftools-search-string-separator) "\\(.*\\)") link)
+                                (match-string 1 link)))
+                (desc (funcall org-pdftools-get-desc-function file page (or quot isearchstr))))
+           (org-link-store-props
+            :type org-pdftools-link-prefix
+            :link link
+            :description desc)))
+        ((eq major-mode 'pdf-occur-buffer-mode)
+         (let* ((paths (mapconcat #'identity (mapcar #'car
+                         pdf-occur-search-documents) "%&%"))
+                (occur-search-string pdf-occur-search-string)
+                (link (concat org-pdftools-link-prefix ":"
+                       paths "@@" occur-search-string)))
+           (org-link-store-props
+            :type org-pdftools-link-prefix
+            :link link
+            :description (concat "Search: " occur-search-string))))))
+
+;;;###autoload
+(defun org-pdftools-export (link description format)
+  "Export the pdfview LINK with DESCRIPTION for FORMAT from Org files."
+  (let* (path loc page)
+    (if (string-match "\\(.+\\)::\\(.*\\)" link)
+        (progn
+          (setq path (match-string 1 link))
+          (setq loc (match-string 2 link))
+          (if (string-match "\\([0-9]+\\)++\\(.*\\)" loc)
+              (setq page (match-string 1 loc))
+            (setq page loc)))
+      (setq path link))
+
+    ;; `org-export-file-uri` expands the filename correctly
+    (setq path (org-export-file-uri (org-link-escape path)))
+
+    (cond ((eq format 'html)
+           (format
+            "<a href=\"%s#page=%s\">%s</a>"
+            path
+            page
+            description))
+          ((eq format 'latex)
+           (format
+            "\\href{%s}{%s}"
+            path
+            description))
+          ((eq format 'ascii)
+           (format "%s (%s)" description path))
+          (t path))))
+
+;;;###autoload
+(defun org-pdftools-setup-link (&optional prefix)
+  "Set up pdf: links in org-mode."
+  (setq org-pdftools-prefix (or prefix org-pdftools-link-prefix))
+  (org-link-set-parameters org-pdftools-prefix
+                           :follow #'org-pdftools-open
+                           :complete #'org-pdftools-complete-link
+                           :store #'org-pdftools-store-link
+                           :export #'org-pdftools-export))
+
+;;;###autoload
+(defun org-pdftools-complete-link (&optional arg)
+  "Use the existing file name completion for file.
+Links to get the file name, then ask the user for the page number
+and append it. ARG is passed to `org-link-complete-file'."
+  (concat
+   (replace-regexp-in-string
+    "^file:"
+    (concat org-pdftools-link-prefix ":")
+    (org-link-complete-file arg))
+   "::"
+   (read-from-minibuffer
+    "Page:"
+    "1")))
+
+(provide 'org-pdftools)
+;;; org-pdftools.el ends here