Make the db caching more efficient for gpg encrypted files (#963)

Before this patch all hash-sums were computed over the files or
buffers content.  For encrypted files this means that we first have
decrypt the file before we can compute the hash-sum.  So when the
cache get's updated all gpg files need to be decrypted which is a very
expensive operation and nearly defeats the purpose of having a cache
in the first place (for gpg files).

This changes the computation of hash-sums for gpg encrypted files.
Instead of the content the raw files on disk will be read.

This shouldn't interfere with the current use of hashes.

There is one ugly (but otherwise inconsequential) ward, though.
For open buffers of to be gpg encrypted files we need to compute the
hash sum over the contents as well.  This is because there is
no (easy) way to get the encrypted version.  The consequence is that
that buffers file will be rehashed again (then using the bytes on
disk).  But all other non changed gpg files will only be hashed once,
as desired.

Co-authored-by: Jethro Kuan <jethrokuan95@gmail.com>

org-roam-db.el

@@ -49,6 +49,7 @@
 (declare-function org-roam--extract-links                  "org-roam")
 (declare-function org-roam--list-all-files                 "org-roam")
 (declare-function org-roam--path-to-slug                   "org-roam")
+(declare-function org-roam--file-name-extension            "org-roam")
 (declare-function org-roam-buffer--update-maybe            "org-roam-buffer")
 
 ;;;; Options
@@ -367,6 +368,26 @@ connections, nil is returned."
          (files (mapcar 'car-safe (emacsql (org-roam-db) query file max-distance))))
     files))
 
+(defun org-roam-db--file-hash (&optional file-path)
+  "Compute the hash of FILE-PATH, a file or current buffer."
+  (let* ((file-p (and file-path))
+         (file-path (or file-path
+                        (buffer-file-name (current-buffer))))
+         (encrypted-p (and file-path
+                           (string= (org-roam--file-name-extension file-path)
+                                    "gpg"))))
+    (cond ((and encrypted-p file-p)
+           (with-temp-buffer
+             (set-buffer-multibyte nil)
+             (insert-file-contents-literally file-path)
+             (secure-hash 'sha1 (current-buffer))))
+          (file-p
+           (with-temp-buffer
+             (insert-file-contents file-path)
+             (secure-hash 'sha1 (current-buffer))))
+          (t
+           (secure-hash 'sha1 (current-buffer))))))
+
 ;;;;; Updating
 (defun org-roam-db--update-meta ()
   "Update the metadata of the current buffer into the cache."
@@ -374,7 +395,7 @@ connections, nil is returned."
          (attr (file-attributes file))
          (atime (file-attribute-access-time attr))
          (mtime (file-attribute-modification-time attr))
-         (hash (secure-hash 'sha1 (current-buffer))))
+         (hash (org-roam-db--file-hash)))
     (org-roam-db-query [:delete :from files
                         :where (= file $s1)]
                        file)
@@ -468,10 +489,10 @@ If FORCE, force a rebuild of the cache from scratch."
         (let* ((attr (file-attributes file))
                (atime (file-attribute-access-time attr))
                (mtime (file-attribute-modification-time attr)))
-          (org-roam--with-temp-buffer file
+          (let ((contents-hash (org-roam-db--file-hash file)))
-            (let ((contents-hash (secure-hash 'sha1 (current-buffer))))
             (unless (string= (gethash file current-files)
                              contents-hash)
+              (org-roam--with-temp-buffer file
                (org-roam-db--clear-file file)
                (org-roam-db-query
                 [:insert :into files
@@ -483,10 +504,10 @@ If FORCE, force a rebuild of the cache from scratch."
                    (setq headline-count (1+ headline-count)))))))))
       ;; Second step: Rebuild the rest
       (dolist (file org-roam-files)
-        (org-roam--with-temp-buffer file
+        (let ((contents-hash (org-roam-db--file-hash file)))
-          (let ((contents-hash (secure-hash 'sha1 (current-buffer))))
           (unless (string= (gethash file current-files)
                            contents-hash)
+            (org-roam--with-temp-buffer file
              (when-let (links (org-roam--extract-links file))
                (org-roam-db-query
                 [:insert :into links
@@ -505,8 +526,8 @@ If FORCE, force a rebuild of the cache from scratch."
                (setq title-count (+ title-count (length titles))))
              (when-let* ((ref (org-roam--extract-ref)))
                (when (org-roam-db--insert-ref file ref)
-                  (setq ref-count (1+ ref-count)))))
+                 (setq ref-count (1+ ref-count))))))
-            (remhash file current-files))))
+          (remhash file current-files)))
       (dolist (file (hash-table-keys current-files))
         ;; These files are no longer around, remove from cache...
         (org-roam-db--clear-file file)