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...about undefined functions or unused lexical variables. Undefined functions: for example, s.el and org-element should be `require`'d when their functions are used. Unused lexical variables: if Org isn't loaded yet, dynamic variables defined in org.el would be treated as lexical and byte-comp would emit this warning. This is especially important in the future as native-comp / gccemacs will optimize away unused lexical variables, and we cannot rely on Org having been implicitly loaded before our modules are compiled. Explicitly stating in our modules that the variables are dynamic prevents that.
566 lines
23 KiB
EmacsLisp
566 lines
23 KiB
EmacsLisp
;;; org-roam-db.el --- Org-roam database API -*- coding: utf-8; lexical-binding: t; -*-
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;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
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;; Author: Jethro Kuan <jethrokuan95@gmail.com>
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;; URL: https://github.com/org-roam/org-roam
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;; Keywords: org-mode, roam, convenience
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;; Version: 1.2.2
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;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
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;; This file is NOT part of GNU Emacs.
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;; This program is free software; you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation; either version 3, or (at your option)
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;; any later version.
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;;
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;; This program is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;;
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;; You should have received a copy of the GNU General Public License
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;; along with GNU Emacs; see the file COPYING. If not, write to the
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;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
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;; Boston, MA 02110-1301, USA.
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;;; Commentary:
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;;
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;; This library is provides the underlying database api to org-roam
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;;
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;;; Code:
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;;;; Library Requires
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(eval-when-compile (require 'subr-x))
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(require 'emacsql)
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(require 'emacsql-sqlite3)
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(require 'seq)
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(eval-and-compile
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(require 'org-roam-macs)
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;; For `org-with-wide-buffer'
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(require 'org-macs))
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(defvar org-roam-directory)
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(defvar org-roam-enable-headline-linking)
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(defvar org-roam-verbose)
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(defvar org-roam-file-name)
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(defvar org-agenda-files)
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(declare-function org-roam--org-roam-file-p "org-roam")
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(declare-function org-roam--extract-titles "org-roam")
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(declare-function org-roam--extract-ref "org-roam")
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(declare-function org-roam--extract-tags "org-roam")
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(declare-function org-roam--extract-ids "org-roam")
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(declare-function org-roam--extract-links "org-roam")
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(declare-function org-roam--list-all-files "org-roam")
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(declare-function org-roam--path-to-slug "org-roam")
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(declare-function org-roam--file-name-extension "org-roam")
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(declare-function org-roam-buffer--update-maybe "org-roam-buffer")
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;;;; Options
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(defcustom org-roam-db-location (expand-file-name "org-roam.db" user-emacs-directory)
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"The full path to file where the Org-roam database is stored.
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If this is non-nil, the Org-roam sqlite database is saved here.
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It is the user's responsibility to set this correctly, especially
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when used with multiple Org-roam instances."
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:type 'string
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:group 'org-roam)
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(defcustom org-roam-db-gc-threshold gc-cons-threshold
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"The value to temporarily set the `gc-cons-threshold' threshold to.
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During large, heavy operations like `org-roam-db-build-cache',
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many GC operations happen because of the large number of
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temporary structures generated (e.g. parsed ASTs). Temporarily
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increasing `gc-cons-threshold' will help reduce the number of GC
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operations, at the cost of temporary memory usage.
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This defaults to the original value of `gc-cons-threshold', but
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tweaking this number may lead to better overall performance. For
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example, to reduce the number of GCs, one may set it to a large
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value like `most-positive-fixnum'."
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:type 'int
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:group 'org-roam)
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(defconst org-roam-db--version 10)
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(defvar org-roam-db--connection (make-hash-table :test #'equal)
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"Database connection to Org-roam database.")
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(defvar org-roam-db-dirty nil
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"Whether the org-roam database is dirty and requires an update.
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Contains pairs of `org-roam-directory' and `org-roam-db-location'
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so that multi-directories are updated.")
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;;;; Core Functions
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(defun org-roam-db--get-connection ()
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"Return the database connection, if any."
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(gethash (expand-file-name org-roam-directory)
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org-roam-db--connection))
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(defun org-roam-db ()
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"Entrypoint to the Org-roam sqlite database.
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Initializes and stores the database, and the database connection.
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Performs a database upgrade when required."
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(unless (and (org-roam-db--get-connection)
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(emacsql-live-p (org-roam-db--get-connection)))
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(let ((init-db (not (file-exists-p org-roam-db-location))))
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(make-directory (file-name-directory org-roam-db-location) t)
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(let ((conn (emacsql-sqlite3 org-roam-db-location)))
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(set-process-query-on-exit-flag (emacsql-process conn) nil)
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(puthash (expand-file-name org-roam-directory)
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conn
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org-roam-db--connection)
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(when init-db
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(org-roam-db--init conn))
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(let* ((version (caar (emacsql conn "PRAGMA user_version")))
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(version (org-roam-db--update-maybe conn version)))
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(cond
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((> version org-roam-db--version)
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(emacsql-close conn)
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(user-error
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"The Org-roam database was created with a newer Org-roam version. "
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"You need to update the Org-roam package"))
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((< version org-roam-db--version)
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(emacsql-close conn)
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(error "BUG: The Org-roam database scheme changed %s"
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"and there is no upgrade path")))))))
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(org-roam-db--get-connection))
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;;;; Entrypoint: (org-roam-db-query)
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(defun org-roam-db-query (sql &rest args)
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"Run SQL query on Org-roam database with ARGS.
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SQL can be either the emacsql vector representation, or a string."
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(if (stringp sql)
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(emacsql (org-roam-db) (apply #'format sql args))
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(apply #'emacsql (org-roam-db) sql args)))
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;;;; Schemata
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(defconst org-roam-db--table-schemata
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'((files
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[(file :unique :primary-key)
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(hash :not-null)
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(meta :not-null)])
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(ids
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[(id :unique :primary-key)
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(file :not-null)
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(level :not-null)])
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(links
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[(source :not-null)
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(dest :not-null)
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(type :not-null)
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(properties :not-null)])
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(tags
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[(file :unique :primary-key)
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(tags)])
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(titles
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[(file :not-null)
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title])
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(refs
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[(ref :unique :not-null)
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(file :not-null)
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(type :not-null)])))
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(defun org-roam-db--init (db)
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"Initialize database DB with the correct schema and user version."
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(emacsql-with-transaction db
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(pcase-dolist (`(,table . ,schema) org-roam-db--table-schemata)
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(emacsql db [:create-table $i1 $S2] table schema))
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(emacsql db (format "PRAGMA user_version = %s" org-roam-db--version))))
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(defun org-roam-db--update-maybe (db version)
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"Upgrades the database schema for DB, if VERSION is old."
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(emacsql-with-transaction db
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'ignore
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(if (< version org-roam-db--version)
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(progn
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(org-roam-message (format "Upgrading the Org-roam database from version %d to version %d"
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version org-roam-db--version))
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(org-roam-db-build-cache t))))
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version)
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(defun org-roam-db--close (&optional db)
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"Closes the database connection for database DB.
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If DB is nil, closes the database connection for the database in
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the current `org-roam-directory'."
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(unless db
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(setq db (org-roam-db--get-connection)))
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(when (and db (emacsql-live-p db))
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(emacsql-close db)))
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(defun org-roam-db--close-all ()
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"Closes all database connections made by Org-roam."
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(dolist (conn (hash-table-values org-roam-db--connection))
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(org-roam-db--close conn)))
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(defun org-roam-db--mark-dirty ()
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"Mark the Org-roam database as dirty."
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(add-to-list 'org-roam-db-dirty (list org-roam-directory org-roam-db-location)
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nil #'equal))
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;;;; Database API
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;;;;; Initialization
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(defun org-roam-db--initialized-p ()
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"Whether the Org-roam cache has been initialized."
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(and (file-exists-p org-roam-db-location)
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(> (caar (org-roam-db-query [:select (funcall count) :from titles]))
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0)))
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(defun org-roam-db--ensure-built ()
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"Ensures that Org-roam cache is built."
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(unless (org-roam-db--initialized-p)
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(error "[Org-roam] your cache isn't built yet! Please run org-roam-db-build-cache")))
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;;;;; Clearing
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(defun org-roam-db-clear ()
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"Clears all entries in the Org-roam cache."
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(interactive)
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(when (file-exists-p org-roam-db-location)
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(dolist (table (mapcar #'car org-roam-db--table-schemata))
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(org-roam-db-query `[:delete :from ,table]))))
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(defun org-roam-db--clear-file (&optional filepath)
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"Remove any related links to the file at FILEPATH.
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This is equivalent to removing the node from the graph."
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(let ((file (expand-file-name (or filepath
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(buffer-file-name (buffer-base-buffer))))))
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(dolist (table (mapcar #'car org-roam-db--table-schemata))
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(org-roam-db-query `[:delete :from ,table
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:where (= ,(if (eq table 'links) 'source 'file) $s1)]
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file))))
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;;;;; Inserting
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(defun org-roam-db--insert-meta (&optional update-p)
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"Update the metadata of the current buffer into the cache.
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If UPDATE-P is non-nil, first remove the meta for the file in the database."
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(let* ((file (or org-roam-file-name (buffer-file-name)))
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(attr (file-attributes file))
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(atime (file-attribute-access-time attr))
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(mtime (file-attribute-modification-time attr))
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(hash (org-roam-db--file-hash)))
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(when update-p
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(org-roam-db-query [:delete :from files
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:where (= file $s1)]
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file))
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(org-roam-db-query
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[:insert :into files
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:values $v1]
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(list (vector file hash (list :atime atime :mtime mtime))))))
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(defun org-roam-db--insert-titles (&optional update-p)
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"Update the titles of the current buffer into the cache.
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If UPDATE-P is non-nil, first remove titles for the file in the database.
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Returns the number of rows inserted."
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(let* ((file (or org-roam-file-name (buffer-file-name)))
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(titles (or (org-roam--extract-titles)
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(list (org-roam--path-to-slug file))))
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(rows (mapcar (lambda (title)
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(vector file title)) titles)))
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(when update-p
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(org-roam-db-query [:delete :from titles
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:where (= file $s1)]
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file))
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(org-roam-db-query
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[:insert :into titles
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:values $v1]
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rows)
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(length rows)))
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(defun org-roam-db--insert-ref (&optional update-p)
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"Update the ref of the current buffer into the cache.
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If UPDATE-P is non-nil, first remove the ref for the file in the database."
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(let ((file (or org-roam-file-name (buffer-file-name))))
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(when update-p
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(org-roam-db-query [:delete :from refs
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:where (= file $s1)]
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file))
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(if-let ((ref (org-roam--extract-ref)))
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(let ((key (cdr ref))
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(type (car ref)))
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(condition-case nil
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(progn
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(org-roam-db-query
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[:insert :into refs :values $v1]
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(list (vector key file type)))
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1)
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(error
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(lwarn '(org-roam) :error
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(format "Duplicate ref %s in:\n\nA: %s\nB: %s\n\nskipping..."
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key
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file
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(caar (org-roam-db-query
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[:select file :from refs
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:where (= ref $v1)]
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(vector key)))))
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0)))
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0)))
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(defun org-roam-db--insert-links (&optional update-p)
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"Update the file links of the current buffer in the cache.
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If UPDATE-P is non-nil, first remove the links for the file in the database.
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Return the number of rows inserted."
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(let ((file (or org-roam-file-name (buffer-file-name))))
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(when update-p
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(org-roam-db-query [:delete :from links
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:where (= source $s1)]
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file))
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(if-let ((links (org-roam--extract-links)))
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(progn
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(org-roam-db-query
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[:insert :into links
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:values $v1]
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links)
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(length links))
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0)))
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(defun org-roam-db--insert-ids (&optional update-p)
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"Update the ids of the current buffer into the cache.
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If UPDATE-P is non-nil, first remove ids for the file in the database.
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Returns the number of rows inserted."
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(let ((file (or org-roam-file-name (buffer-file-name))))
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(when update-p
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(org-roam-db-query [:delete :from ids
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:where (= file $s1)]
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file))
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(if-let ((ids (org-roam--extract-ids file)))
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(condition-case nil
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(progn
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(org-roam-db-query
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[:insert :into ids
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:values $v1]
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ids)
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(length ids))
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(error
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(lwarn '(org-roam) :error
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(format "Duplicate IDs in %s, one of:\n\n%s\n\nskipping..."
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(aref (car ids) 1)
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(string-join (mapcar (lambda (hl)
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(aref hl 0)) ids) "\n")))
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0))
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0)))
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(defun org-roam-db--insert-tags (&optional update-p)
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"Insert tags for the current buffer into the Org-roam cache.
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If UPDATE-P is non-nil, first remove tags for the file in the database.
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Return the number of rows inserted."
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(let* ((file (or org-roam-file-name (buffer-file-name)))
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(tags (org-roam--extract-tags file)))
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(when update-p
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(org-roam-db-query [:delete :from tags
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:where (= file $s1)]
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file))
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(if tags
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(progn (org-roam-db-query
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[:insert :into tags
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:values $v1]
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(list (vector file tags)))
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1)
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0)))
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;;;;; Fetching
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(defun org-roam-db--get-current-files ()
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"Return a hash-table of file to the hash of its file contents."
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(let* ((current-files (org-roam-db-query [:select * :from files]))
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(ht (make-hash-table :test #'equal)))
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(dolist (row current-files)
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(puthash (car row) (cadr row) ht))
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ht))
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(defun org-roam-db--get-titles (file)
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"Return the titles of FILE from the cache."
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(caar (org-roam-db-query [:select [title] :from titles
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:where (= file $s1)
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:limit 1]
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file)))
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(defun org-roam-db--get-tags ()
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"Return all distinct tags from the cache."
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(let ((rows (org-roam-db-query [:select :distinct [tags] :from tags]))
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acc)
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(dolist (row rows)
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(dolist (tag (car row))
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(unless (member tag acc)
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(push tag acc))))
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acc))
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(defun org-roam-db--connected-component (file)
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"Return all files reachable from/connected to FILE, including the file itself.
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If the file does not have any connections, nil is returned."
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(let* ((query "WITH RECURSIVE
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links_of(file, link) AS
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(WITH filelinks AS (SELECT * FROM links WHERE NOT \"type\" = '\"cite\"'),
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citelinks AS (SELECT * FROM links
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JOIN refs ON links.\"dest\" = refs.\"ref\"
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AND links.\"type\" = '\"cite\"')
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SELECT \"source\", \"dest\" FROM filelinks UNION
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SELECT \"dest\", \"source\" FROM filelinks UNION
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SELECT \"file\", \"source\" FROM citelinks UNION
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SELECT \"dest\", \"file\" FROM citelinks),
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connected_component(file) AS
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(SELECT link FROM links_of WHERE file = $s1
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UNION
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SELECT link FROM links_of JOIN connected_component USING(file))
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SELECT * FROM connected_component;")
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(files (mapcar 'car-safe (emacsql (org-roam-db) query file))))
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files))
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(defun org-roam-db--links-with-max-distance (file max-distance)
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"Return all files connected to FILE in at most MAX-DISTANCE steps.
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This includes the file itself. If the file does not have any
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connections, nil is returned."
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(let* ((query "WITH RECURSIVE
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links_of(file, link) AS
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(WITH filelinks AS (SELECT * FROM links WHERE NOT \"type\" = '\"cite\"'),
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citelinks AS (SELECT * FROM links
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JOIN refs ON links.\"dest\" = refs.\"ref\"
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AND links.\"type\" = '\"cite\"')
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SELECT \"source\", \"dest\" FROM filelinks UNION
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SELECT \"dest\", \"source\" FROM filelinks UNION
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SELECT \"file\", \"source\" FROM citelinks UNION
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SELECT \"source\", \"file\" FROM citelinks),
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-- Links are traversed in a breadth-first search. In order to calculate the
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-- distance of nodes and to avoid following cyclic links, the visited nodes
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-- are tracked in 'trace'.
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connected_component(file, trace) AS
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(VALUES($s1, json_array($s1))
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UNION
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SELECT lo.link, json_insert(cc.trace, '$[' || json_array_length(cc.trace) || ']', lo.link) FROM
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connected_component AS cc JOIN links_of AS lo USING(file)
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WHERE (
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-- Avoid cycles by only visiting each file once.
|
|
(SELECT count(*) FROM json_each(cc.trace) WHERE json_each.value == lo.link) == 0
|
|
-- Note: BFS is cut off early here.
|
|
AND json_array_length(cc.trace) < ($s2 + 1)))
|
|
SELECT DISTINCT file, min(json_array_length(trace)) AS distance
|
|
FROM connected_component GROUP BY file ORDER BY distance;")
|
|
;; In principle the distance would be available in the second column.
|
|
(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."
|
|
(if file-path
|
|
(with-temp-buffer
|
|
(set-buffer-multibyte nil)
|
|
(insert-file-contents-literally file-path)
|
|
(secure-hash 'sha1 (current-buffer)))
|
|
(org-with-wide-buffer
|
|
(secure-hash 'sha1 (current-buffer)))))
|
|
|
|
;;;;; Updating
|
|
(defun org-roam-db--update-file (&optional file-path)
|
|
"Update Org-roam cache for FILE-PATH.
|
|
If the file does not exist anymore, remove it from the cache.
|
|
If the file exists, update the cache with information."
|
|
(setq file-path (or file-path
|
|
(buffer-file-name (buffer-base-buffer))))
|
|
(if (not (file-exists-p file-path))
|
|
(org-roam-db--clear-file file-path)
|
|
;; save the file before performing a database update
|
|
(when-let ((buf (find-buffer-visiting file-path)))
|
|
(with-current-buffer buf
|
|
(save-buffer)))
|
|
(org-roam--with-temp-buffer file-path
|
|
(emacsql-with-transaction (org-roam-db)
|
|
(org-roam-db--insert-meta 'update)
|
|
(org-roam-db--insert-tags 'update)
|
|
(org-roam-db--insert-titles 'update)
|
|
(org-roam-db--insert-ref 'update)
|
|
(when org-roam-enable-headline-linking
|
|
(org-roam-db--insert-ids 'update))
|
|
(org-roam-db--insert-links 'update)))))
|
|
|
|
(defun org-roam-db-build-cache (&optional force)
|
|
"Build the cache for `org-roam-directory'.
|
|
If FORCE, force a rebuild of the cache from scratch."
|
|
(interactive "P")
|
|
(when force (delete-file org-roam-db-location))
|
|
(org-roam-db--close) ;; Force a reconnect
|
|
(org-roam-db) ;; To initialize the database, no-op if already initialized
|
|
(let* ((gc-cons-threshold org-roam-db-gc-threshold)
|
|
(org-agenda-files nil)
|
|
(org-roam-files (org-roam--list-all-files))
|
|
(current-files (org-roam-db--get-current-files))
|
|
(id-count 0)
|
|
(link-count 0)
|
|
(tag-count 0)
|
|
(title-count 0)
|
|
(ref-count 0)
|
|
(deleted-count 0)
|
|
(modified-count 0)
|
|
(modified-files nil))
|
|
(dolist (file org-roam-files)
|
|
(let ((contents-hash (org-roam-db--file-hash file)))
|
|
(unless (string= (gethash file current-files)
|
|
contents-hash)
|
|
(push (cons file contents-hash) modified-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)
|
|
(setq deleted-count (1+ deleted-count)))
|
|
(pcase-dolist (`(,file . _) modified-files)
|
|
(org-roam-db--clear-file file))
|
|
;; Process all the files for IDs first
|
|
;;
|
|
;; We do this so that link extraction is cheaper: this eliminates the need
|
|
;; to read the file to check if the ID really exists
|
|
(pcase-dolist (`(,file . ,contents-hash) modified-files)
|
|
(let* ((attr (file-attributes file))
|
|
(atime (file-attribute-access-time attr))
|
|
(mtime (file-attribute-modification-time attr)))
|
|
(condition-case nil
|
|
(org-roam--with-temp-buffer file
|
|
(org-roam-db-query
|
|
[:insert :into files
|
|
:values $v1]
|
|
(vector file contents-hash (list :atime atime :mtime mtime)))
|
|
(when org-roam-enable-headline-linking
|
|
(setq id-count (+ id-count (org-roam-db--insert-ids)))))
|
|
(file-error
|
|
(setq org-roam-files (remove file org-roam-files))
|
|
(org-roam-db--clear-file file)
|
|
(lwarn '(org-roam) :warning
|
|
"Skipping unreadable file while building cache: %s" file)))))
|
|
(pcase-dolist (`(,file . _) modified-files)
|
|
(org-roam-message "Processed %s/%s modified files..." modified-count (length modified-files))
|
|
(condition-case nil
|
|
(org-roam--with-temp-buffer file
|
|
(setq modified-count (1+ modified-count))
|
|
(setq link-count (+ link-count (org-roam-db--insert-links)))
|
|
(setq tag-count (+ tag-count (org-roam-db--insert-tags)))
|
|
(setq title-count (+ title-count (org-roam-db--insert-titles)))
|
|
(setq ref-count (+ ref-count (org-roam-db--insert-ref))))
|
|
(file-error
|
|
(setq org-roam-files (remove file org-roam-files))
|
|
(org-roam-db--clear-file file)
|
|
(lwarn '(org-roam) :warning
|
|
"Skipping unreadable file while building cache: %s" file))))
|
|
(org-roam-message "total: Δ%s, files-modified: Δ%s, ids: Δ%s, links: Δ%s, tags: Δ%s, titles: Δ%s, refs: Δ%s, deleted: Δ%s"
|
|
(length org-roam-files)
|
|
modified-count
|
|
id-count
|
|
link-count
|
|
tag-count
|
|
title-count
|
|
ref-count
|
|
deleted-count)))
|
|
|
|
(defun org-roam-db-update-cache ()
|
|
"Update the cache if the database is dirty."
|
|
(pcase-dolist (`(,org-roam-directory ,org-roam-db-location) org-roam-db-dirty)
|
|
(org-roam-db-build-cache))
|
|
(setq org-roam-db-dirty nil))
|
|
|
|
(provide 'org-roam-db)
|
|
|
|
;;; org-roam-db.el ends here
|