[PATCH] Re: [BUG] org-cite: 10 second hang opening a ~4k org file with 10MB bibtex library

[Ihor Radchenko <yantar92@gmail.com>]

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Jamie Matthews <jdm204@cam.ac.uk> writes:

> I can confirm that the key turns red on insert when I altered the key outside of emacs (with that second version of `org-cite-basic--parse-bibliography`).

Great. Then, I am attaching the patch with the new version of the
function. I will let Nicolas decide if it is good enough to be merged. I
do not feel confident enough with org-cite code to judge if my approach
is not missing some edge cases.

> However, I'm now noticing that the hang improvement earlier (< a second down from ~10) doesn't always occur.
>
> Specifically, if I
>
>   1.  emacs -Q
>   2.  eval your code in scratch
>   3.  C-x C-f to the org file
>
> I get the hang. However, if I then
>
>
>   1.  kill the org buffer
>   2.  eval the code again
>   3.  re-find the org file
>
> the hang is gone. Without eval​ing your code in between, killing the org buffer and finding it again in the same emacs session reproduces the hang everytime, which was probably what I did the first time I report the improvement, as in I didn't check it worked from startup.

It is most likely because you defun the function after emacs -Q before
org is loaded, then open Org file (opening Org file autoloads org-mode),
and then org-mode overwrites the manual defun.
If I am correct, putting (require 'oc-basic) before defun will fix what
you are seeing.

Best,
Ihor


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From 100b722708c68bc65af637c3ad4e289943cccd7c Mon Sep 17 00:00:00 2001
Message-Id: <100b722708c68bc65af637c3ad4e289943cccd7c.1647690044.git.yantar92@gmail.com>
From: Ihor Radchenko <yantar92@gmail.com>
Date: Sat, 19 Mar 2022 19:24:55 +0800
Subject: [PATCH] oc-basic: Speed up cached bibliography retrival

* lisp/oc-basic.el (org-cite-basic--file-id-cache): New variable
storing hash of bibliography file contents.
(org-cite-basic--parse-bibliography): Skip buffer hash calculation
when bibliography file is unchanged on disk.  Calculating buffer hash
on every call is slow when bibliography file is large.

* lisp/org-compat.el:
(org-file-has-changed-p--hash-table, org-file-has-changed-p): Define
`file-has-changed-p' from Emacs 29 if necessary.

See https://list.orgmode.org/LO2P265MB1758E12E04832DC712F5A8E9DC149@LO2P265MB1758.GBRP265.PROD.OUTLOOK.COM/T/#t
---
 lisp/oc-basic.el   | 11 +++++++++--
 lisp/org-compat.el | 29 +++++++++++++++++++++++++++++
 2 files changed, 38 insertions(+), 2 deletions(-)

diff --git a/lisp/oc-basic.el b/lisp/oc-basic.el
index e2dfc0603..d1ea620ad 100644
--- a/lisp/oc-basic.el
+++ b/lisp/oc-basic.el
@@ -233,6 +233,8 @@ (defun org-cite-basic--parse-bibtex (dialect)
                 entries)))
     entries))
 
+(defvar org-cite-basic--file-id-cache nil
+  "Hash table linking files to their hash.")
 (defun org-cite-basic--parse-bibliography (&optional info)
   "List all entries available in the buffer.
 
@@ -245,14 +247,19 @@ (defun org-cite-basic--parse-bibliography (&optional info)
 as symbols, and values as strings or nil.
 
 Optional argument INFO is the export state, as a property list."
+  (unless (hash-table-p org-cite-basic--file-id-cache)
+    (setq org-cite-basic--file-id-cache (make-hash-table :test #'equal)))
   (if (plist-member info :cite-basic/bibliography)
       (plist-get info :cite-basic/bibliography)
     (let ((results nil))
       (dolist (file (org-cite-list-bibliography-files))
         (when (file-readable-p file)
           (with-temp-buffer
-            (insert-file-contents file)
-	    (let* ((file-id (cons file (org-buffer-hash)))
+            (when (or (org-file-has-changed-p file)
+                      (not (gethash file org-cite-basic--file-id-cache)))
+              (insert-file-contents file)
+              (puthash file (org-buffer-hash) org-cite-basic--file-id-cache))
+	    (let* ((file-id (cons file (gethash file org-cite-basic--file-id-cache)))
                    (entries
                     (or (cdr (assoc file-id org-cite-basic--bibliography-cache))
                         (let ((table
diff --git a/lisp/org-compat.el b/lisp/org-compat.el
index 38d330de6..e96dcba8b 100644
--- a/lisp/org-compat.el
+++ b/lisp/org-compat.el
@@ -73,6 +73,35 @@ (defvar org-table-dataline-regexp)
 (defvar org-table-tab-recognizes-table.el)
 (defvar org-table1-hline-regexp)
 
+\f
+;;; Emacs < 29 compatibility
+
+(defvar org-file-has-changed-p--hash-table (make-hash-table :test #'equal)
+  "Internal variable used by `org-file-has-changed-p'.")
+
+(if (fboundp 'file-has-changed-p)
+    (defalias org-file-has-changed-p #'file-has-changed-p)
+  (defun org-file-has-changed-p (file &optional tag)
+    "Return non-nil if FILE has changed.
+The size and modification time of FILE are compared to the size
+and modification time of the same FILE during a previous
+invocation of `org-file-has-changed-p'.  Thus, the first invocation
+of `org-file-has-changed-p' always returns non-nil when FILE exists.
+The optional argument TAG, which must be a symbol, can be used to
+limit the comparison to invocations with identical tags; it can be
+the symbol of the calling function, for example."
+    (let* ((file (directory-file-name (expand-file-name file)))
+           (remote-file-name-inhibit-cache t)
+           (fileattr (file-attributes file 'integer))
+	   (attr (and fileattr
+                      (cons (file-attribute-size fileattr)
+		            (file-attribute-modification-time fileattr))))
+	   (sym (concat (symbol-name tag) "@" file))
+	   (cachedattr (gethash sym org-file-has-changed-p--hash-table)))
+      (when (not (equal attr cachedattr))
+        (puthash sym attr org-file-has-changed-p--hash-table)))))
+
+
 \f
 ;;; Emacs < 28.1 compatibility
 
-- 
2.34.1