emacsql-sqlite3 -> emacsql-sqlite

Revert from emacsql-sqlite3 to emacsql-sqlite for foreign key support.
This makes it slightly harder to get Org-roam up and running for
Windows, but not impossible, but foreign keys makes database operations
faster and keeps the code clean.

Also, fix schemata for foreign keys on various tables, and add indices
where joins are common (org-roam-db--table-indices).

org-roam-capture.el

@@ -6,7 +6,7 @@
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
 ;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 

org-roam-compat.el

@@ -6,7 +6,7 @@
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
 ;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 

org-roam-completion.el

@@ -6,7 +6,7 @@
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
 ;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 ;; This file is NOT part of GNU Emacs.
 
 ;; This program is free software; you can redistribute it and/or modify

org-roam-dailies.el

@@ -8,7 +8,7 @@
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
 ;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 

org-roam-db.el

@@ -6,7 +6,7 @@
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
 ;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -33,7 +33,7 @@
 ;;;; Library Requires
 (eval-when-compile (require 'subr-x))
 (require 'emacsql)
-(require 'emacsql-sqlite3)
+(require 'emacsql-sqlite)
 (require 'seq)
 
 (eval-and-compile
@@ -79,7 +79,7 @@ value like `most-positive-fixnum'."
   :type 'int
   :group 'org-roam)
 
-(defconst org-roam-db--version 13)
+(defconst org-roam-db--version 14)
 
 (defvar org-roam-db--connection (make-hash-table :test #'equal)
   "Database connection to Org-roam database.")
@@ -99,7 +99,7 @@ Performs a database upgrade when required."
                (emacsql-live-p (org-roam-db--get-connection)))
     (let ((init-db (not (file-exists-p org-roam-db-location))))
       (make-directory (file-name-directory org-roam-db-location) t)
-      (let ((conn (emacsql-sqlite3 org-roam-db-location)))
+      (let ((conn (emacsql-sqlite org-roam-db-location)))
         (set-process-query-on-exit-flag (emacsql-process conn) nil)
         (puthash (expand-file-name org-roam-directory)
                  conn
@@ -136,46 +136,47 @@ SQL can be either the emacsql vector representation, or a string."
       (hash :not-null)])
 
     (nodes
-     [(id :primary-key :not-null)
-      (file :not-null)
-      (level :not-null)
-      (pos :not-null)
-      todo
-      priority
-      (scheduled text)
-      (deadline text)
-      title
-      properties
-      olp]
-     (:foreign-key [file] :references files [file] :on-delete :cascade))
+     ([(id :not-null :primary-key)
+       (file :not-null)
+       (level :not-null)
+       (pos :not-null)
+       todo
+       priority
+       (scheduled text)
+       (deadline text)
+       title
+       properties
+       olp]
+      (:foreign-key [file] :references files [file] :on-delete :cascade)))
 
     (aliases
-     [(file :not-null)
-      (node-id :not-null)
-      alias]
-     (:foreign-key [node-id] :references nodes [id] :on-delete :cascade))
+     ([(node-id :not-null :primary-key)
+       alias]
+      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
 
     (refs
-     ([(file :not-null)
-       (node-id :not-null)
+     ([(node-id :not-null)
        (ref :not-null)
        (type :not-null)]
       (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
 
     (tags
-     [(file :not-null)
-      (node-id :not-null)
+     ([(node-id :not-null)
       tag]
-     (:foreign-key [node-id] :references nodes [id] :on-delete :cascade))
+      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
 
     (links
-     [(file :not-null)
-      (pos :not-null)
-      (source :not-null)
-      (dest :not-null)
-      (type :not-null)
-      (properties :not-null)]
-     (:foreign-key [file] :references files [file] :on-delete :cascade))))
+     ([(pos :not-null)
+       (source :not-null)
+       (dest :not-null)
+       (type :not-null)
+       (properties :not-null)]
+      (:foreign-key [source] :references nodes [id] :on-delete :cascade)))))
+
+(defconst org-roam-db--table-indices
+  '((alias-node-id aliases [node-id])
+    (refs-node-id refs [node-id])
+    (tags-node-id tags [node-id])))
 
 (defun org-roam-db--init (db)
   "Initialize database DB with the correct schema and user version."
@@ -183,6 +184,8 @@ SQL can be either the emacsql vector representation, or a string."
     (emacsql db "PRAGMA foreign_keys = ON")
     (pcase-dolist (`(,table ,schema) org-roam-db--table-schemata)
       (emacsql db [:create-table $i1 $S2] table schema))
+    (pcase-dolist (`(,index-name ,table ,columns) org-roam-db--table-indices)
+      (emacsql db [:create-index $i1 :on $i2 $S3] index-name table columns))
     (emacsql db (format "PRAGMA user_version = %s" org-roam-db--version))))
 
 (defun org-roam-db--upgrade-maybe (db version)
@@ -224,10 +227,9 @@ the current `org-roam-directory'."
 This is equivalent to removing the node from the graph.
 If FILE is nil, clear the current buffer."
   (setq file (or file (buffer-file-name (buffer-base-buffer))))
-  (dolist (table (mapcar #'car org-roam-db--table-schemata))
-    (org-roam-db-query `[:delete :from ,table
-                         :where (= file $s1)]
-                       file)))
+  (org-roam-db-query [:delete :from files
+                      :where (= file $s1)]
+                     file))
 
 ;;;;; Updating tables
 (defun org-roam-db-insert-file ()
@@ -297,14 +299,14 @@ If UPDATE-P is non-nil, first remove the file in the database."
              [:insert :into tags
               :values $v1]
              (mapcar (lambda (tag)
-                       (vector file id (substring-no-properties tag)))
+                       (vector id (substring-no-properties tag)))
                      tags)))
           (when aliases
             (org-roam-db-query
              [:insert :into aliases
               :values $v1]
              (mapcar (lambda (alias)
-                       (vector file id alias))
+                       (vector id alias))
                      (split-string-and-unquote aliases))))
           (when refs
             (setq refs (split-string-and-unquote refs))
@@ -312,7 +314,7 @@ If UPDATE-P is non-nil, first remove the file in the database."
               (dolist (ref refs)
                 (if (string-match org-link-plain-re ref)
                     (progn
-                      (push (vector file id (match-string 2 ref)
+                      (push (vector id (match-string 2 ref)
                                     (match-string 1 ref)) rows))
                   (lwarn '(org-roam) :warning
                          "%s:%s\tInvalid ref %s, skipping..."
@@ -356,18 +358,16 @@ If UPDATE-P is non-nil, first remove the file in the database."
 
 (defun org-roam-db-insert-tags ()
   "Insert tags for node at point into Org-roam cache."
-  (when-let ((file (buffer-file-name (buffer-base-buffer)))
-             (node-id (org-id-get))
+  (when-let ((node-id (org-id-get))
              (tags (org-get-tags)))
     (org-roam-db-query [:insert :into tags
                         :values $v1]
                        (mapcar (lambda (tag)
-                                 (vector file node-id tag)) tags))))
+                                 (vector node-id tag)) tags))))
 
 (defun org-roam-db-insert-refs ()
   "Insert refs for node at point into Org-roam cache."
-  (when-let* ((file (buffer-file-name (buffer-base-buffer)))
-              (node-id (org-id-get))
+  (when-let* ((node-id (org-id-get))
               (refs (org-entry-get (point) "ROAM_REFS"))
               (refs (split-string-and-unquote refs)))
     (let (rows)
@@ -375,7 +375,7 @@ If UPDATE-P is non-nil, first remove the file in the database."
         (save-match-data
           (if (string-match org-link-plain-re ref)
               (progn
-                (push (vector file node-id (match-string 2 ref) (match-string 1 ref)) rows))
+                (push (vector node-id (match-string 2 ref) (match-string 1 ref)) rows))
             (lwarn '(org-roam) :warning
                    "%s:%s\tInvalid ref %s, skipping..." (buffer-file-name) (point) ref))))
       (org-roam-db-query [:insert :into refs
@@ -386,8 +386,7 @@ If UPDATE-P is non-nil, first remove the file in the database."
   "Insert link data for LINK at current point into the Org-roam cache."
   (save-excursion
     (goto-char (org-element-property :begin link))
-    (let ((file (buffer-file-name (buffer-base-buffer)))
-          (type (org-element-property :type link))
+    (let ((type (org-element-property :type link))
           (dest (org-element-property :path link))
           (properties (list :outline (org-get-outline-path)))
           (source (org-roam-id-at-point)))
@@ -395,7 +394,7 @@ If UPDATE-P is non-nil, first remove the file in the database."
         (org-roam-db-query
          [:insert :into links
           :values $v1]
-         (vector file (point) source dest type properties))))))
+         (vector (point) source dest type properties))))))
 
 ;;;;; Fetching
 (defun org-roam-db--get-current-files ()

org-roam-doctor.el

@@ -6,7 +6,7 @@
 ;; URL: https://github.com/jethrokuan/org-roam
 ;; Keywords: org-mode, roam, convenience
 ;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 

org-roam-macs.el

@@ -6,7 +6,7 @@
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
 ;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 

org-roam-mode.el

@@ -5,7 +5,7 @@
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
 ;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 

org-roam-protocol.el

@@ -5,7 +5,7 @@
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
 ;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 

org-roam-refile.el

@@ -6,7 +6,7 @@
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
 ;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 

org-roam-utils.el

@@ -6,7 +6,7 @@
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
 ;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 

org-roam.el

@@ -6,7 +6,7 @@
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
 ;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.