From b8bd6fd1b014bd572756bd46e8ccc74857f70c89 Mon Sep 17 00:00:00 2001
From: Kaitlin Newson <kaitlin.newson@gmail.com>
Date: Mon, 23 Sep 2024 14:16:37 -0300
Subject: [PATCH] #10189 Convert Queries to an Eloquent Model (#10384)

* pkp/pkp-lib#10189 Convert Queries to an Eloquent Model

* pkp/pkp-lib#10189 Convert Queries to an Eloquent Model

* pkp/pkp-lib#10189 Convert Queries to an Eloquent Model

* pkp/pkp-lib#10189 cleanup indentation issues

* pkp/pkp-lib#10189 review feedback

* pkp/pkp-lib#10189 review feedback
---
 classes/controllers/grid/GridHandler.php      |  25 +-
 classes/core/PKPApplication.php               |   5 +-
 .../types/traits/IsRecommendation.php         |  14 +-
 classes/facades/Repo.php                      |  12 +-
 classes/note/Note.php                         |   2 +-
 classes/note/Repository.php                   |  29 +-
 ...ingProductionStatusNotificationManager.php |  30 +-
 .../QueryNotificationManager.php              |  34 +-
 classes/query/Query.php                       | 155 +++---
 classes/query/QueryDAO.php                    | 490 ------------------
 classes/query/QueryParticipant.php            |  88 ++++
 classes/query/Repository.php                  | 199 +++++++
 .../authorization/NoteAccessPolicy.php        |  15 +-
 .../QueryAssignedToUserAccessPolicy.php       |  25 +-
 .../internal/QueryRequiredPolicy.php          |  17 +-
 ...ubmissionFileAssignedQueryAccessPolicy.php |  28 +-
 classes/submission/DAO.php                    |  10 +-
 classes/submission/Repository.php             |   9 +-
 classes/submission/maps/Schema.php            |   9 +-
 classes/submissionFile/Repository.php         |  11 +-
 ...ubmissionFilesCategoryGridDataProvider.php |  11 +-
 .../query/ManageQueryNoteFilesGridHandler.php |   9 +-
 .../query/QueryNoteFilesGridDataProvider.php  |  11 +-
 .../files/query/QueryNoteFilesGridHandler.php |   6 +-
 .../NotificationsGridCellProvider.php         |  15 +-
 .../grid/queries/QueriesAccessHelper.php      |  30 +-
 .../grid/queries/QueriesGridCellProvider.php  |  15 +-
 .../grid/queries/QueriesGridHandler.php       | 105 ++--
 .../grid/queries/QueryNotesGridHandler.php    |  25 +-
 .../grid/queries/QueryNotesGridRow.php        |   3 +-
 .../grid/queries/QueryTitleGridColumn.php     |   9 +-
 controllers/grid/queries/form/QueryForm.php   | 116 +++--
 .../grid/queries/form/QueryNoteForm.php       |  37 +-
 .../form/PKPStageParticipantNotifyForm.php    |  45 +-
 .../controllers/grid/queries/readQuery.tpl    |   6 +-
 35 files changed, 719 insertions(+), 931 deletions(-)
 delete mode 100644 classes/query/QueryDAO.php
 create mode 100644 classes/query/QueryParticipant.php
 create mode 100644 classes/query/Repository.php

diff --git a/classes/controllers/grid/GridHandler.php b/classes/controllers/grid/GridHandler.php
index c897f9c0ee4..50c62ef9184 100644
--- a/classes/controllers/grid/GridHandler.php
+++ b/classes/controllers/grid/GridHandler.php
@@ -40,6 +40,7 @@
 namespace PKP\controllers\grid;
 
 use APP\template\TemplateManager;
+use Illuminate\Database\Eloquent\Model;
 use Illuminate\Support\Enumerable;
 use Illuminate\Support\LazyCollection;
 use Illuminate\Support\Str;
@@ -47,6 +48,7 @@
 use PKP\core\ItemIterator;
 use PKP\core\JSONMessage;
 use PKP\core\PKPRequest;
+use PKP\db\DAOResultFactory;
 use PKP\db\DBResultRange;
 use PKP\form\Form;
 use PKP\handler\PKPHandler;
@@ -398,17 +400,12 @@ public function setGridDataElements($data)
     {
         $this->callFeaturesHook('setGridDataElements', ['grid' => &$this, 'data' => &$data]);
 
-        if ($data instanceof Enumerable) {
-            $this->_data = $this->toAssociativeArray($data);
-        } elseif (is_iterable($data)) {
-            $this->_data = $data;
-        } elseif ($data instanceof \PKP\db\DAOResultFactory) {
-            $this->_data = $data->toAssociativeArray();
-        } elseif ($data instanceof ItemIterator) {
-            $this->_data = $data->toArray();
-        } else {
-            assert(false);
-        }
+        $this->_data = match (true) {
+            $data instanceof Enumerable => $this->toAssociativeArray($data),
+            $data instanceof DAOResultFactory => $data->toAssociativeArray(),
+            $data instanceof ItemIterator => $data->toArray(),
+            is_iterable($data) => $data
+        };
     }
 
     /**
@@ -1378,7 +1375,11 @@ public static function toAssociativeArray(LazyCollection $lazyCollection, string
     {
         $returner = [];
         foreach ($lazyCollection as $item) {
-            $returner[$item->getData($idField)] = $item;
+            if ($item instanceof Model) {
+                $returner[$item->$idField] = $item;
+            } else {
+                $returner[$item->getData($idField)] = $item;
+            }
         }
         return $returner;
     }
diff --git a/classes/core/PKPApplication.php b/classes/core/PKPApplication.php
index 65f8f071997..47b9ac1d545 100644
--- a/classes/core/PKPApplication.php
+++ b/classes/core/PKPApplication.php
@@ -3,8 +3,8 @@
 /**
  * @file classes/core/PKPApplication.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class PKPApplication
@@ -487,7 +487,6 @@ public function getDAOMap(): array
             'SubmissionCommentDAO' => 'PKP\submission\SubmissionCommentDAO',
             'SubmissionDisciplineDAO' => 'PKP\submission\SubmissionDisciplineDAO',
             'SubmissionDisciplineEntryDAO' => 'PKP\submission\SubmissionDisciplineEntryDAO',
-            'QueryDAO' => 'PKP\query\QueryDAO',
             'SubmissionKeywordDAO' => 'PKP\submission\SubmissionKeywordDAO',
             'SubmissionKeywordEntryDAO' => 'PKP\submission\SubmissionKeywordEntryDAO',
             'SubmissionSubjectDAO' => 'PKP\submission\SubmissionSubjectDAO',
diff --git a/classes/decision/types/traits/IsRecommendation.php b/classes/decision/types/traits/IsRecommendation.php
index 30fd7de48ca..72035e2e27a 100644
--- a/classes/decision/types/traits/IsRecommendation.php
+++ b/classes/decision/types/traits/IsRecommendation.php
@@ -2,8 +2,8 @@
 /**
  * @file classes/decision/types/traits/IsRecommendation.php
  *
- * Copyright (c) 2014-2022 Simon Fraser University
- * Copyright (c) 2000-2022 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class decision
@@ -31,7 +31,7 @@
 use PKP\mail\Mailable;
 use PKP\mail\mailables\RecommendationNotifyEditors;
 use PKP\note\Note;
-use PKP\query\QueryDAO;
+use PKP\query\Query;
 use PKP\security\Role;
 use PKP\stageAssignment\StageAssignment;
 use PKP\submission\reviewRound\ReviewRound;
@@ -132,9 +132,7 @@ protected function addRecommendationQuery(EmailData $email, Submission $submissi
             }
         }
 
-        /** @var QueryDAO $queryDao */
-        $queryDao = DAORegistry::getDAO('QueryDAO');
-        $queryId = $queryDao->addQuery(
+        $queryId = Repo::query()->addQuery(
             $submission->getId(),
             $this->getStageId(),
             $email->subject,
@@ -145,8 +143,8 @@ protected function addRecommendationQuery(EmailData $email, Submission $submissi
             false
         );
 
-        $query = $queryDao->getById($queryId);
-        $note = $query->getHeadNote();
+        $query = Query::find($queryId);
+        $note = Repo::note()->getHeadNote($query->id);
         $mailable = new Mailable();
         foreach ($email->attachments as $attachment) {
             if (isset($attachment[Mailable::ATTACHMENT_TEMPORARY_FILE])) {
diff --git a/classes/facades/Repo.php b/classes/facades/Repo.php
index cbfb448f7d1..70ae1392cb7 100644
--- a/classes/facades/Repo.php
+++ b/classes/facades/Repo.php
@@ -3,8 +3,8 @@
 /**
  * @file classes/facades/Repo.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class Repo
@@ -38,7 +38,8 @@
 use PKP\log\event\Repository as EventLogRepository;
 use PKP\log\Repository as EmailLogEntryRepository;
 use PKP\note\Repository as NoteRepository;
-use PKP\notification\Notification as NotificationRepository;
+use PKP\notification\Repository as NotificationRepository;
+use PKP\query\Repository as QueryRepository;
 use PKP\stageAssignment\Repository as StageAssignmentRepository;
 use PKP\submissionFile\Repository as SubmissionFileRepository;
 use PKP\userGroup\Repository as UserGroupRepository;
@@ -134,4 +135,9 @@ public static function note(): NoteRepository
     {
         return app(NoteRepository::class);
     }
+
+    public static function query(): QueryRepository
+    {
+        return app(QueryRepository::class);
+    }
 }
diff --git a/classes/note/Note.php b/classes/note/Note.php
index 092fad325e1..2f8cc726a25 100644
--- a/classes/note/Note.php
+++ b/classes/note/Note.php
@@ -101,7 +101,7 @@ public function getData(?string $field)
      */
     public function scopeWithUserId(Builder $query, int $userId): Builder
     {
-        return $query->where('userId', $userId);
+        return $query->where('user_id', $userId);
     }
 
     /**
diff --git a/classes/note/Repository.php b/classes/note/Repository.php
index 78fa1ef6b7e..68857620ac8 100644
--- a/classes/note/Repository.php
+++ b/classes/note/Repository.php
@@ -16,27 +16,24 @@
 
 namespace PKP\note;
 
+use PKP\db\DAO;
+use PKPApplication;
+
 class Repository
 {
-    /**
-     * Fetch a note by symbolic info, building it if needed.
-     */
-    public function build(int $assocType, int $assocId, int $userId, ?string $contents, ?string $title): Note
-    {
-        return Note::withUserId($userId)
-            ->withAssoc($assocType, $assocId)
-            ->firstOr(fn() => Note::create([
-                'assocType' => $assocType,
-                'assocId' => $assocId,
-                'userId' => $userId,
-                'contents' => $contents,
-                'title' => $title,
-            ]));
-    }
-
     public function transfer(int $oldUserId, int $newUserId): int
     {
         return Note::withUserId($oldUserId)
             ->update(['user_id' => $newUserId]);
     }
+
+    /**
+     * Get the "head" (first) note for a Query.
+     */
+    public function getHeadNote(int $queryId): ?Note
+    {
+        return Note::withAssoc(PKPApplication::ASSOC_TYPE_QUERY, $queryId)
+            ->withSort(Note::NOTE_ORDER_DATE_CREATED, DAO::SORT_DIRECTION_ASC)
+            ->first();
+    }
 }
diff --git a/classes/notification/managerDelegate/PKPEditingProductionStatusNotificationManager.php b/classes/notification/managerDelegate/PKPEditingProductionStatusNotificationManager.php
index f172a0b0877..c84de4a6fb2 100644
--- a/classes/notification/managerDelegate/PKPEditingProductionStatusNotificationManager.php
+++ b/classes/notification/managerDelegate/PKPEditingProductionStatusNotificationManager.php
@@ -3,15 +3,15 @@
 /**
  * @file classes/notification/managerDelegate/PKPEditingProductionStatusNotificationManager.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2003-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2003-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class PKPEditingProductionStatusNotificationManager
  *
- * @ingroup classses_notification_managerDelegate
+ * @ingroup classes_notification_managerDelegate
  *
- * @brief Editing and productionstatus notifications types manager delegate.
+ * @brief Editing and production status notifications types manager delegate.
  */
 
 namespace PKP\notification\managerDelegate;
@@ -21,9 +21,9 @@
 use APP\notification\NotificationManager;
 use PKP\core\PKPApplication;
 use PKP\core\PKPRequest;
-use PKP\db\DAORegistry;
 use PKP\notification\Notification;
 use PKP\notification\NotificationManagerDelegate;
+use PKP\query\Query;
 use PKP\security\Role;
 use PKP\stageAssignment\StageAssignment;
 use PKP\submissionFile\SubmissionFile;
@@ -35,7 +35,7 @@ class PKPEditingProductionStatusNotificationManager extends NotificationManagerD
      */
     public function getNotificationMessage(PKPRequest $request, Notification $notification): string|array|null
     {
-        return match($notification->type) {
+        return match ($notification->type) {
             Notification::NOTIFICATION_TYPE_ASSIGN_COPYEDITOR => __('notification.type.assignCopyeditors'),
             Notification::NOTIFICATION_TYPE_AWAITING_COPYEDITS => __('notification.type.awaitingCopyedits'),
             Notification::NOTIFICATION_TYPE_ASSIGN_PRODUCTIONUSER => __('notification.type.assignProductionUser'),
@@ -91,10 +91,10 @@ public function updateNotification(PKPRequest $request, ?array $userIds, int $as
             ->withRoleIds([Role::ROLE_ID_MANAGER, Role::ROLE_ID_SUB_EDITOR])
             ->get();
 
-        // Get the copyediting and production discussions
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var \PKP\query\QueryDAO $queryDao */
-        $productionQueries = $queryDao->getByAssoc(Application::ASSOC_TYPE_SUBMISSION, $submissionId, WORKFLOW_STAGE_ID_PRODUCTION);
-        $productionQuery = $productionQueries->next();
+        // Get the production discussions
+        $productionQuery = Query::withAssoc(Application::ASSOC_TYPE_SUBMISSION, $submissionId)
+            ->withStageId(WORKFLOW_STAGE_ID_PRODUCTION)
+            ->first();
 
         // Get the copyedited files
         $countCopyeditedFiles = Repo::submissionFile()
@@ -165,8 +165,10 @@ public function updateNotification(PKPRequest $request, ?array $userIds, int $as
                         $this->_removeNotification($submissionId, $editorStageAssignment->userId, $notificationType, $contextId);
                     } else {
                         // If a copyeditor is assigned i.e. there is a copyediting discussion
-                        $editingQueries = $queryDao->getByAssoc(Application::ASSOC_TYPE_SUBMISSION, $submissionId, WORKFLOW_STAGE_ID_EDITING);
-                        if ($editingQueries->next()) {
+                        $editingQueries = Query::withAssoc(Application::ASSOC_TYPE_SUBMISSION, $submissionId)
+                            ->withStageId(WORKFLOW_STAGE_ID_EDITING)
+                            ->first();
+                        if ($editingQueries) {
                             if ($notificationType == Notification::NOTIFICATION_TYPE_AWAITING_COPYEDITS) {
                                 // Add 'awaiting copyedits' notification
                                 $this->_createNotification(
@@ -239,7 +241,3 @@ public function _createNotification(PKPRequest $request, int $submissionId, int
         }
     }
 }
-
-if (!PKP_STRICT_MODE) {
-    class_alias('\PKP\notification\managerDelegate\PKPEditingProductionStatusNotificationManager', '\PKPEditingProductionStatusNotificationManager');
-}
diff --git a/classes/notification/managerDelegate/QueryNotificationManager.php b/classes/notification/managerDelegate/QueryNotificationManager.php
index 87e7e0e4082..0d1d8dbebae 100644
--- a/classes/notification/managerDelegate/QueryNotificationManager.php
+++ b/classes/notification/managerDelegate/QueryNotificationManager.php
@@ -23,13 +23,10 @@
 use PKP\core\PKPApplication;
 use PKP\core\PKPRequest;
 use PKP\core\PKPString;
-use PKP\db\DAO;
-use PKP\db\DAORegistry;
 use PKP\note\Note;
 use PKP\notification\Notification;
 use PKP\notification\NotificationManagerDelegate;
 use PKP\query\Query;
-use PKP\query\QueryDAO;
 
 class QueryNotificationManager extends NotificationManagerDelegate
 {
@@ -41,10 +38,9 @@ public function getNotificationMessage(PKPRequest $request, Notification $notifi
         if ($notification->assocType != Application::ASSOC_TYPE_QUERY) {
             throw new \Exception('Unexpected assoc type!');
         }
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $query = $queryDao->getById($notification->assocId);
+        $query = Query::find($notification->assocId);
 
-        $headNote = $query->getHeadNote();
+        $headNote = Repo::note()->getHeadNote($query->id);
         if (!$headNote) {
             throw new \Exception('Unable to retrieve head note for query!');
         }
@@ -58,14 +54,14 @@ public function getNotificationMessage(PKPRequest $request, Notification $notifi
                     'noteTitle' => Str::limit($headNote->title, 200),
                 ]);
             case Notification::NOTIFICATION_TYPE_QUERY_ACTIVITY:
-                $latestNote = Note::withAssoc(PKPApplication::ASSOC_TYPE_QUERY, $query->getAssocId())
+                $latestNote = Note::withAssoc(PKPApplication::ASSOC_TYPE_QUERY, $query->id)
                     ->withSort(Note::NOTE_ORDER_ID)
                     ->first();
                 $user = $latestNote->user;
                 return __('submission.query.activity', [
                     'responderName' => $user->getFullName(),
                     'noteContents' => Str::limit(PKPString::html2text($latestNote->contents), 200),
-                    'noteTitle' => Str::limit($headNote->title,200),
+                    'noteTitle' => Str::limit($headNote->title, 200),
                 ]);
         }
         throw new \Exception('Unexpected notification type!');
@@ -76,12 +72,12 @@ public function getNotificationMessage(PKPRequest $request, Notification $notifi
      */
     protected function getQuerySubmission(Query $query): Submission
     {
-        switch ($query->getAssocType()) {
+        switch ($query->assocType) {
             case Application::ASSOC_TYPE_SUBMISSION:
-                return Repo::submission()->get($query->getAssocId());
+                return Repo::submission()->get($query->assocId);
             case Application::ASSOC_TYPE_REPRESENTATION:
                 $representationDao = Application::getRepresentationDAO();
-                $representation = $representationDao->getById($query->getAssocId());
+                $representation = $representationDao->getById($query->assocId);
                 $publication = Repo::publication()->get($representation->getData('publicationId'));
                 return Repo::submission()->get($publication->getData('submissionId'));
         }
@@ -97,8 +93,7 @@ public function getNotificationUrl(PKPRequest $request, Notification $notificati
             throw new \Exception('Unexpected query assoc type!');
         }
 
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $query = $queryDao->getById($notification->assocId);
+        $query = Query::find($notification->assocId);
         if (!$query) {
             return null;
         }
@@ -112,11 +107,10 @@ public function getNotificationUrl(PKPRequest $request, Notification $notificati
      */
     public function getNotificationContents(PKPRequest $request, Notification $notification): mixed
     {
-        if($notification->assocType != Application::ASSOC_TYPE_QUERY) {
+        if ($notification->assocType != Application::ASSOC_TYPE_QUERY) {
             throw new \Exception('Unexpected assoc type!');
         }
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $query = $queryDao->getById($notification->assocId);
+        $query = Query::find($notification->assocId);
         $submission = $this->getQuerySubmission($query);
 
         switch ($notification->type) {
@@ -124,7 +118,7 @@ public function getNotificationContents(PKPRequest $request, Notification $notif
                 return __(
                     'submission.query.new.contents',
                     [
-                        'queryTitle' => $query->getHeadNote()->title,
+                        'queryTitle' => Repo::note()->getHeadNote($query->id)->title,
                         'submissionTitle' => $submission->getCurrentPublication()->getLocalizedTitle(null, 'html'),
                     ]
                 );
@@ -132,7 +126,7 @@ public function getNotificationContents(PKPRequest $request, Notification $notif
                 return __(
                     'submission.query.activity.contents',
                     [
-                        'queryTitle' => $query->getHeadNote()->title,
+                        'queryTitle' => Repo::note()->getHeadNote($query->id)->title,
                         'submissionTitle' => $submission->getCurrentPublication()->getLocalizedTitle(null, 'html'),
                     ]
                 );
@@ -148,7 +142,3 @@ public function getStyleClass(Notification $notification): string
         return NOTIFICATION_STYLE_CLASS_WARNING;
     }
 }
-
-if (!PKP_STRICT_MODE) {
-    class_alias('\PKP\notification\managerDelegate\QueryNotificationManager', '\QueryNotificationManager');
-}
diff --git a/classes/query/Query.php b/classes/query/Query.php
index aa1d8e20664..8997b8d9259 100644
--- a/classes/query/Query.php
+++ b/classes/query/Query.php
@@ -3,142 +3,131 @@
 /**
  * @file classes/query/Query.php
  *
- * Copyright (c) 2016-2024 Simon Fraser University
- * Copyright (c) 2003-2024 John Willinsky
+ * Copyright (c) 2024 Simon Fraser University
+ * Copyright (c) 2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class Query
  *
- * @ingroup submission
- *
- * @see QueryDAO
- *
  * @brief Class for Query.
  */
 
 namespace PKP\query;
 
-use Illuminate\Support\LazyCollection;
-use PKP\core\PKPApplication;
-use PKP\db\DAORegistry;
-use PKP\db\DAO;
-use PKP\note\Note;
+use APP\facades\Repo;
+use Eloquence\Behaviours\HasCamelCasing;
+use Illuminate\Database\Eloquent\Builder;
+use Illuminate\Database\Eloquent\Casts\Attribute;
+use Illuminate\Database\Eloquent\Model;
+use Illuminate\Database\Eloquent\Relations\HasMany;
 
-class Query extends \PKP\core\DataObject
+class Query extends Model
 {
-    /**
-     * Get query assoc type
-     *
-     * @return int Application::ASSOC_TYPE_...
-     */
-    public function getAssocType()
-    {
-        return $this->getData('assocType');
-    }
+    use HasCamelCasing;
 
-    /**
-     * Set query assoc type
-     *
-     * @param int $assocType Application::ASSOC_TYPE_...
-     */
-    public function setAssocType($assocType)
-    {
-        $this->setData('assocType', $assocType);
-    }
+    const CREATED_AT = 'date_posted';
+    const UPDATED_AT = 'date_modified';
 
-    /**
-     * Get query assoc ID
-     *
-     * @return int
-     */
-    public function getAssocId()
+    protected $table = 'queries';
+    protected $primaryKey = 'query_id';
+
+    protected $fillable = [
+        'assocType', 'assocId', 'stageId', 'seq',
+        'datePosted', 'dateModified', 'closed'
+    ];
+
+    protected function casts(): array
     {
-        return $this->getData('assocId');
+        return [
+            'assocType' => 'int',
+            'assocId' => 'int',
+            'stageId' => 'int',
+            'seq' => 'float',
+            'datePosted' => 'datetime',
+            'dateModified' => 'datetime',
+            'closed' => 'boolean'
+        ];
     }
 
     /**
-     * Set query assoc ID
-     *
-     * @param int $assocId
+     * Accessor and Mutator for primary key => id
      */
-    public function setAssocId($assocId)
+    protected function id(): Attribute
     {
-        $this->setData('assocId', $assocId);
+        return Attribute::make(
+            get: fn($value, $attributes) => $attributes[$this->primaryKey] ?? null,
+            set: fn($value) => [$this->primaryKey => $value],
+        );
     }
 
     /**
-     * Get stage ID
-     *
-     * @return int
+     * Accessor for users. Can be replaced with relationship once User is converted to an Eloquent Model.
      */
-    public function getStageId()
+    protected function users(): Attribute
     {
-        return $this->getData('stageId');
+        return Attribute::make(
+            get: function () {
+                $userIds = $this->queryParticipants()
+                    ->pluck('user_id')
+                    ->all();
+                return Repo::user()->getCollector()->filterByUserIds($userIds)->getMany();
+            },
+        );
     }
 
     /**
-     * Set stage ID
-     *
-     * @param int $stageId
+     * Relationship to Query Participants. Can be replaced with Many-to-Many relationship once
+     * User is converted to an Eloquent Model.
      */
-    public function setStageId($stageId)
+    public function queryParticipants(): HasMany
     {
-        return $this->setData('stageId', $stageId);
+        return $this->hasMany(QueryParticipant::class, 'query_id', 'query_id');
     }
 
+    // Scopes
+
     /**
-     * Get sequence of query.
-     *
-     * @return float
+     * Scope a query to only include queries with a specific assoc type and assoc ID.
      */
-    public function getSequence()
+    public function scopeWithAssoc(Builder $query, int $assocType, int $assocId): Builder
     {
-        return $this->getData('sequence');
+        return $query->where('assoc_type', $assocType)
+            ->where('assoc_id', $assocId);
     }
 
     /**
-     * Set sequence of query.
-     *
-     * @param float $sequence
+     * Scope a query to only include queries with a specific stage ID.
      */
-    public function setSequence($sequence)
+    public function scopeWithStageId(Builder $query, int $stageId): Builder
     {
-        $this->setData('sequence', $sequence);
+        return $query->where('stage_id', $stageId);
     }
 
     /**
-     * Get closed flag
-     *
-     * @return bool
+     * Scope a query to only include queries with a specific closed status.
      */
-    public function getIsClosed()
+    public function scopeWithClosed(Builder $query, bool $closed): Builder
     {
-        return $this->getData('closed');
+        return $query->where('closed', $closed);
     }
 
     /**
-     * Set closed flag
-     *
-     * @param bool $isClosed
+     * Scope a query to only include queries with a specific user ID.
      */
-    public function setIsClosed($isClosed)
+    public function scopeWithUserId(Builder $query, int $userId): Builder
     {
-        return $this->setData('closed', $isClosed);
+        return $query->whereHas('queryParticipants', function ($q) use ($userId) {
+            $q->where('user_id', $userId);
+        });
     }
 
     /**
-     * Get the "head" (first) note for this query.
-     *
-     * @return Note
+     * Scope a query to only include queries with specific user IDs.
      */
-    public function getHeadNote()
+    public function scopeWithUserIds($query, array $userIds)
     {
-        return Note::withAssoc(PKPApplication::ASSOC_TYPE_QUERY, $this->getId())
-            ->withSort(Note::NOTE_ORDER_DATE_CREATED, DAO::SORT_DIRECTION_ASC)
-            ->first();
+        return $query->whereHas('queryParticipants', function ($q) use ($userIds) {
+            $q->whereIn('user_id', $userIds);
+        });
     }
 }
-
-if (!PKP_STRICT_MODE) {
-    class_alias('\PKP\query\Query', '\Query');
-}
diff --git a/classes/query/QueryDAO.php b/classes/query/QueryDAO.php
deleted file mode 100644
index e1734f520ce..00000000000
--- a/classes/query/QueryDAO.php
+++ /dev/null
@@ -1,490 +0,0 @@
-<?php
-
-/**
- * @file classes/query/QueryDAO.php
- *
- * Copyright (c) 2016-2024 Simon Fraser University
- * Copyright (c) 2000-2024 John Willinsky
- * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
- *
- * @class QueryDAO
- *
- * @ingroup query
- *
- * @see Query
- *
- * @brief Operations for retrieving and modifying Query objects.
- */
-
-namespace PKP\query;
-
-use APP\core\Application;
-use APP\facades\Repo;
-use APP\notification\NotificationManager;
-use APP\submission\Submission;
-use Illuminate\Database\Query\Builder;
-use Illuminate\Support\Facades\DB;
-use Illuminate\Support\Facades\Mail;
-use PKP\db\DAO;
-use PKP\db\DAORegistry;
-use PKP\db\DAOResultFactory;
-use PKP\mail\Mailable;
-use PKP\note\Note;
-use PKP\notification\Notification;
-use PKP\notification\NotificationSubscriptionSettingsDAO;
-use PKP\plugins\Hook;
-use PKP\security\Role;
-use PKP\stageAssignment\StageAssignment;
-use PKP\user\User;
-
-class QueryDAO extends DAO
-{
-    /**
-     * Retrieve a submission query by ID.
-     *
-     * @param int $queryId Query ID
-     * @param int $assocType Optional Application::ASSOC_TYPE_...
-     * @param int $assocId Optional assoc ID per assocType
-     *
-     * @return Query
-     */
-    public function getById($queryId, $assocType = null, $assocId = null)
-    {
-        $params = [(int) $queryId];
-        if ($assocType) {
-            $params[] = (int) $assocType;
-            $params[] = (int) $assocId;
-        }
-        $result = $this->retrieve(
-            'SELECT *
-			FROM	queries
-			WHERE	query_id = ?'
-                . ($assocType ? ' AND assoc_type = ? AND assoc_id = ?' : ''),
-            $params
-        );
-        $row = $result->current();
-        return $row ? $this->_fromRow((array) $row) : null;
-    }
-
-    /**
-     * Retrieve all queries by association
-     *
-     * @param int $assocType Application::ASSOC_TYPE_...
-     * @param int $assocId Assoc ID
-     * @param int $stageId Optional stage ID
-     * @param int $userId Optional user ID; when set, show only assigned queries
-     *
-     * @return DAOResultFactory<Query> Query
-     */
-    public function getByAssoc($assocType, $assocId, $stageId = null, $userId = null)
-    {
-        $params = [];
-        $params[] = (int) Application::ASSOC_TYPE_QUERY;
-        if ($userId) {
-            $params[] = (int) $userId;
-        }
-        $params[] = (int) $assocType;
-        $params[] = (int) $assocId;
-        if ($stageId) {
-            $params[] = (int) $stageId;
-        }
-        if ($userId) {
-            $params[] = (int) $userId;
-        }
-
-        return new DAOResultFactory(
-            $this->retrieve(
-                'SELECT	DISTINCT q.*
-				FROM	queries q
-				LEFT JOIN notes n ON n.assoc_type = ? AND n.assoc_id = q.query_id
-				' . ($userId ? 'INNER JOIN query_participants qp ON (q.query_id = qp.query_id AND qp.user_id = ?)' : '') . '
-				WHERE	q.assoc_type = ? AND q.assoc_id = ?
-				' . ($stageId ? ' AND q.stage_id = ?' : '') .
-                ($userId ? '
-				AND (n.user_id = ? OR n.title IS NOT NULL
-				OR n.contents IS NOT NULL)' : '') . '
-				ORDER BY q.seq',
-                $params
-            ),
-            $this,
-            '_fromRow'
-        );
-    }
-
-    /**
-     * Retrieve a count of all open queries totalled by stage
-     *
-     * @param int[] $participantIds Only include queries with these participants
-     *
-     * @return array<int,int> [int $stageId => int $count]
-     */
-    public function countOpenPerStage(int $submissionId, ?array $participantIds = null)
-    {
-        $counts = DB::table('queries as q')
-            ->when($participantIds !== null, function (Builder $q) use ($participantIds) {
-                $q->join('query_participants as qp', 'q.query_id', '=', 'qp.query_id')
-                    ->whereIn('qp.user_id', $participantIds);
-            })
-            ->where('q.assoc_type', '=', Application::ASSOC_TYPE_SUBMISSION)
-            ->where('q.assoc_id', '=', $submissionId)
-            ->where('q.closed', '=', 0)
-            ->select(['q.stage_id', DB::raw('COUNT(q.stage_id) as count')])
-            ->groupBy(['q.stage_id'])
-            ->get()
-            ->mapWithKeys(fn ($row, $key) => [$row->stage_id => $row->count])
-            ->toArray();
-
-        return collect(Application::get()->getApplicationStages())
-            ->mapWithKeys(fn ($stageId, $key) => [$stageId => $counts[$stageId] ?? 0]);
-    }
-
-    /**
-     * Internal function to return a submission query object from a row.
-     *
-     * @param array $row
-     *
-     * @return Query
-     *
-     * @hook QueryDAO::_fromRow [[&$query, &$row]]
-     */
-    public function _fromRow($row)
-    {
-        $query = $this->newDataObject();
-        $query->setId($row['query_id']);
-        $query->setAssocType($row['assoc_type']);
-        $query->setAssocId($row['assoc_id']);
-        $query->setStageId($row['stage_id']);
-        $query->setIsClosed($row['closed']);
-        $query->setSequence($row['seq']);
-
-        Hook::call('QueryDAO::_fromRow', [&$query, &$row]);
-        return $query;
-    }
-
-    /**
-     * Get a new data object
-     *
-     * @return Query
-     */
-    public function newDataObject()
-    {
-        return new Query();
-    }
-
-    /**
-     * Insert a new Query.
-     *
-     * @param Query $query
-     *
-     * @return int New query ID
-     */
-    public function insertObject($query)
-    {
-        $this->update(
-            'INSERT INTO queries (assoc_type, assoc_id, stage_id, closed, seq)
-			VALUES (?, ?, ?, ?, ?)',
-            [
-                (int) $query->getAssocType(),
-                (int) $query->getAssocId(),
-                (int) $query->getStageId(),
-                (int) $query->getIsClosed(),
-                (float) $query->getSequence(),
-            ]
-        );
-        $query->setId($this->getInsertId());
-        return $query->getId();
-    }
-
-    /**
-     * Adds a participant to a query.
-     *
-     * @param int $queryId Query ID
-     * @param int $userId User ID
-     */
-    public function insertParticipant($queryId, $userId)
-    {
-        $this->update(
-            'INSERT INTO query_participants
-			(query_id, user_id)
-			VALUES
-			(?, ?)',
-            [(int) $queryId, (int) $userId]
-        );
-    }
-
-    /**
-     * Removes a participant from a query.
-     *
-     * @param int $queryId Query ID
-     * @param int $userId User ID
-     */
-    public function removeParticipant($queryId, $userId)
-    {
-        $this->update(
-            'DELETE FROM query_participants WHERE query_id = ? AND user_id = ?',
-            [(int) $queryId, (int) $userId]
-        );
-    }
-
-    /**
-     * Removes all participants from a query.
-     *
-     * @param int $queryId Query ID
-     */
-    public function removeAllParticipants($queryId)
-    {
-        $this->update(
-            'DELETE FROM query_participants WHERE query_id = ?',
-            [(int) $queryId]
-        );
-    }
-
-    /**
-     * Retrieve all participant user IDs for a query.
-     *
-     * @param int $queryId Query ID
-     * @param int $userId User ID to restrict results to
-     *
-     * @return array
-     */
-    public function getParticipantIds($queryId, $userId = null)
-    {
-        $params = [(int) $queryId];
-        if ($userId) {
-            $params[] = (int) $userId;
-        }
-        $result = $this->retrieve(
-            'SELECT	user_id
-			FROM	query_participants
-			WHERE	query_id = ?' .
-            ($userId ? ' AND user_id = ?' : ''),
-            $params
-        );
-        $userIds = [];
-        foreach ($result as $row) {
-            $userIds[] = (int) $row->user_id;
-        }
-        return $userIds;
-    }
-
-    /**
-     * Update an existing Query.
-     *
-     * @param Query $query
-     */
-    public function updateObject($query)
-    {
-        $this->update(
-            'UPDATE	queries
-			SET	assoc_type = ?,
-				assoc_id = ?,
-				stage_id = ?,
-				closed = ?,
-				seq = ?
-			WHERE	query_id = ?',
-            [
-                (int) $query->getAssocType(),
-                (int) $query->getAssocId(),
-                (int) $query->getStageId(),
-                (int) $query->getIsClosed(),
-                (float) $query->getSequence(),
-                (int) $query->getId()
-            ]
-        );
-    }
-
-    /**
-     * Delete a submission query.
-     *
-     * @param Query $query
-     */
-    public function deleteObject($query)
-    {
-        $this->deleteById($query->getId());
-    }
-
-    /**
-     * Delete a submission query by ID.
-     *
-     * Deletes any associated notes and notifications. The
-     * participants will be deleted automatically through
-     * the onDelete CASCADE foreign key relationship in
-     * the database table.
-     *
-     * @param $queryId Query ID
-     * @param $assocType Optional Application::ASSOC_TYPE_...
-     * @param $assocId Optional assoc ID per assocType
-     */
-    public function deleteById(int $queryId, ?int $assocType = null, ?int $assocId = null): int
-    {
-        $countDeleted = DB::table('queries')
-            ->where('query_id', '=', $queryId)
-            ->when(!is_null($assocType), function (Builder $q) use ($assocType) {
-                $q->where('assoc_type', '=', $assocType);
-            })
-            ->when(!is_null($assocId), function (Builder $q) use ($assocId) {
-                $q->where('assoc_id', '=', $assocId);
-            })
-            ->delete();
-
-        if ($countDeleted) {
-            Note::withAssoc(Application::ASSOC_TYPE_QUERY, $queryId)->delete();
-            Notification::withAssoc(Application::ASSOC_TYPE_QUERY, $queryId)->delete();
-        }
-
-        return $countDeleted;
-    }
-
-    /**
-     * Sequentially renumber queries in their sequence order.
-     *
-     * @param int $assocType Application::ASSOC_TYPE_...
-     * @param int $assocId Assoc ID per assocType
-     */
-    public function resequence($assocType, $assocId)
-    {
-        $result = $this->retrieve(
-            'SELECT query_id FROM queries WHERE assoc_type = ? AND assoc_id = ? ORDER BY seq',
-            [(int) $assocType, (int) $assocId]
-        );
-
-        for ($i = 1; $row = $result->current(); $i++) {
-            $this->update('UPDATE queries SET seq = ? WHERE query_id = ?', [$i, $row->query_id]);
-            $result->next();
-        }
-    }
-
-    /**
-     * Delete queries by assoc info.
-     *
-     * @param int $assocType Application::ASSOC_TYPE_...
-     * @param int $assocId Assoc ID per assocType
-     */
-    public function deleteByAssoc($assocType, $assocId)
-    {
-        $queries = $this->getByAssoc($assocType, $assocId);
-        while ($query = $queries->next()) {
-            $this->deleteObject($query);
-        }
-    }
-
-    /**
-     * Start a query
-     *
-     * Inserts the query, assigns participants, and creates the head note
-     *
-     * @return int The new query id
-     */
-    public function addQuery(int $submissionId, int $stageId, string $title, string $content, User $fromUser, array $participantUserIds, int $contextId, bool $sendEmail = true): int
-    {
-        $query = $this->newDataObject();
-        $query->setAssocType(Application::ASSOC_TYPE_SUBMISSION);
-        $query->setAssocId($submissionId);
-        $query->setStageId($stageId);
-        $query->setSequence(REALLY_BIG_NUMBER);
-        $this->insertObject($query);
-        $this->resequence(Application::ASSOC_TYPE_SUBMISSION, $submissionId);
-
-        foreach (array_unique($participantUserIds) as $participantUserId) {
-            $this->insertParticipant($query->getId(), $participantUserId);
-        }
-
-        $note = Note::create([
-            'assocType' => Application::ASSOC_TYPE_QUERY,
-            'assocId' => $query->getId(),
-            'contents' => $content,
-            'title' => $title,
-            'userId' => $fromUser->getId(),
-        ]);
-
-        // Add task for assigned participants
-        $notificationMgr = new NotificationManager();
-
-        /** @var NotificationSubscriptionSettingsDAO */
-        $notificationSubscriptionSettingsDao = DAORegistry::getDAO('NotificationSubscriptionSettingsDAO');
-
-        foreach ($participantUserIds as $participantUserId) {
-            $notificationMgr->createNotification(
-                Application::get()->getRequest(),
-                $participantUserId,
-                Notification::NOTIFICATION_TYPE_NEW_QUERY,
-                $contextId,
-                Application::ASSOC_TYPE_QUERY,
-                $query->getId(),
-                Notification::NOTIFICATION_LEVEL_TASK
-            );
-
-            if (!$sendEmail) {
-                continue;
-            }
-
-            // Check if the user is unsubscribed
-            $notificationSubscriptionSettings = $notificationSubscriptionSettingsDao->getNotificationSubscriptionSettings(
-                NotificationSubscriptionSettingsDAO::BLOCKED_EMAIL_NOTIFICATION_KEY,
-                $participantUserId,
-                $contextId
-            );
-            if (in_array(Notification::NOTIFICATION_TYPE_NEW_QUERY, $notificationSubscriptionSettings)) {
-                continue;
-            }
-
-            $recipient = Repo::user()->get($participantUserId);
-            $mailable = new Mailable();
-            $mailable->to($recipient->getEmail(), $recipient->getFullName());
-            $mailable->from($fromUser->getEmail(), $fromUser->getFullName());
-            $mailable->subject($title);
-            $mailable->body($content);
-
-            Mail::send($mailable);
-        }
-
-        return $query->getId();
-    }
-
-    /**
-     * Create a query with a submission's comments for the editors
-     *
-     * Creates the query and assigns all participants
-     *
-     * @return int new query id
-     */
-    public function addCommentsForEditorsQuery(Submission $submission): int
-    {
-        // Replaces StageAssignmentDAO::getBySubmissionAndRoleIds
-        $participantUserIds = StageAssignment::withSubmissionIds([$submission->getId()])
-            ->withRoleIds([
-                Role::ROLE_ID_MANAGER,
-                Role::ROLE_ID_SUB_EDITOR,
-                Role::ROLE_ID_ASSISTANT,
-                Role::ROLE_ID_AUTHOR,
-            ])
-            ->withStageIds([$submission->getData('stageId')])
-            ->get()
-            ->pluck('userId')
-            ->all();
-
-        // Replaces StageAssignmentDAO::getBySubmissionAndRoleIds
-        $authorAssignments = StageAssignment::withSubmissionIds([$submission->getId()])
-            ->withRoleIds([Role::ROLE_ID_AUTHOR])
-            ->withStageIds([$submission->getData('stageId')])
-            ->get();
-
-        $fromUser = $authorAssignments->isEmpty()
-            ? Application::get()->getRequest()->getUser()
-            : Repo::user()->get($authorAssignments->first()->userId);
-
-        return $this->addQuery(
-            $submission->getId(),
-            $submission->getData('stageId'),
-            __('submission.submit.coverNote'),
-            $submission->getData('commentsForTheEditors'),
-            $fromUser,
-            $participantUserIds,
-            $submission->getData('contextId')
-        );
-    }
-}
-
-if (!PKP_STRICT_MODE) {
-    class_alias('\PKP\query\QueryDAO', '\QueryDAO');
-}
diff --git a/classes/query/QueryParticipant.php b/classes/query/QueryParticipant.php
new file mode 100644
index 00000000000..8f09dcf8d8d
--- /dev/null
+++ b/classes/query/QueryParticipant.php
@@ -0,0 +1,88 @@
+<?php
+
+/**
+ * @file classes/query/QueryParticipant.php
+ *
+ * Copyright (c) 2024 Simon Fraser University
+ * Copyright (c) 2024 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class QueryParticipant
+ *
+ * @brief Class for QueryParticipant.
+ */
+
+namespace PKP\query;
+
+use APP\facades\Repo;
+use Eloquence\Behaviours\HasCamelCasing;
+use Illuminate\Database\Eloquent\Builder;
+use Illuminate\Database\Eloquent\Casts\Attribute;
+use Illuminate\Database\Eloquent\Model;
+use Illuminate\Database\Eloquent\Relations\BelongsTo;
+
+class QueryParticipant extends Model
+{
+    use HasCamelCasing;
+
+    protected $table = 'query_participants';
+    protected $primaryKey = 'query_participant_id';
+    public $timestamps = false;
+
+    protected $fillable = [
+        'queryId', 'userId'
+    ];
+
+    protected function casts(): array
+    {
+        return [
+            'queryId' => 'int',
+            'userId' => 'int'
+        ];
+    }
+    public function toQuery(): BelongsTo
+    {
+        return $this->belongsTo(Query::class, 'query_id', 'query_id');
+    }
+
+    /**
+     * Accessor and Mutator for primary key => id
+     */
+    protected function id(): Attribute
+    {
+        return Attribute::make(
+            get: fn($value, $attributes) => $attributes[$this->primaryKey] ?? null,
+            set: fn($value) => [$this->primaryKey => $value],
+        );
+    }
+
+    /**
+     * Accessor for user. Can be replaced with relationship once User is converted to an Eloquent Model.
+     */
+    protected function user(): Attribute
+    {
+        return Attribute::make(
+            get: function () {
+                return Repo::user()->get($this->userId, true);
+            },
+        );
+    }
+
+    // Scopes
+
+    /**
+     * Scope a query to only include query participants with a specific query ID.
+     */
+    public function scopeWithQueryId(Builder $query, int $queryId): Builder
+    {
+        return $query->where('query_id', $queryId);
+    }
+
+    /**
+     * Scope a query to only include query participants with a specific user ID.
+     */
+    public function scopeWithUserId(Builder $query, int $userId): Builder
+    {
+        return $query->where('user_id', $userId);
+    }
+}
diff --git a/classes/query/Repository.php b/classes/query/Repository.php
new file mode 100644
index 00000000000..8713aa60e4a
--- /dev/null
+++ b/classes/query/Repository.php
@@ -0,0 +1,199 @@
+<?php
+
+/**
+ * @file classes/query/Repository.php
+ *
+ * Copyright (c) 2024 Simon Fraser University
+ * Copyright (c) 2024 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class Repository
+ *
+ * @see Query
+ *
+ * @brief Operations for retrieving and modifying Query objects.
+ */
+
+namespace PKP\query;
+
+use APP\core\Application;
+use APP\facades\Repo;
+use APP\notification\NotificationManager;
+use APP\submission\Submission;
+use Illuminate\Support\Facades\Mail;
+use PKP\db\DAORegistry;
+use PKP\mail\Mailable;
+use PKP\note\Note;
+use PKP\notification\Notification;
+use PKP\notification\NotificationSubscriptionSettingsDAO;
+use PKP\security\Role;
+use PKP\stageAssignment\StageAssignment;
+use PKP\user\User;
+
+class Repository
+{
+    /**
+     * Retrieve a count of all open queries totalled by stage
+     *
+     * @param ?int[] $participantIds Only include queries with these participants
+     *
+     * @return array<int,int> [int $stageId => int $count]
+     */
+    public function countOpenPerStage(int $submissionId, ?array $participantIds = null): array
+    {
+        $counts = Query::withAssoc(Application::ASSOC_TYPE_SUBMISSION, $submissionId)
+            ->when($participantIds !== null, function ($q) use ($participantIds) {
+                $q->withUserIds($participantIds);
+            })
+            ->withClosed(false)
+            ->selectRaw('stage_id, COUNT(stage_id) as count')
+            ->groupBy('stage_id')
+            ->get()
+            ->mapWithKeys(fn ($row, $key) => [$row->stage_id => $row->count])
+            ->toArray();
+
+        return collect(Application::get()->getApplicationStages())
+            ->mapWithKeys(fn ($stageId, $key) => [$stageId => $counts[$stageId] ?? 0])
+            ->toArray();
+    }
+
+    /**
+     * Sequentially renumber queries in their sequence order.
+     *
+     * @param int $assocType Application::ASSOC_TYPE_...
+     * @param int $assocId Assoc ID per assocType
+     */
+    public function resequence($assocType, $assocId): void
+    {
+        $result = Query::withAssoc($assocType, $assocId)
+            ->orderBy('seq')
+            ->get();
+
+        $result->each(function (Query $item, int $key = 1) {
+            $item->update(['seq' => $key]);
+        });
+    }
+
+    /**
+     * Start a query
+     *
+     * Inserts the query, assigns participants, and creates the head note
+     *
+     * @return int The new query id
+     */
+    public function addQuery(int $submissionId, int $stageId, string $title, string $content, User $fromUser, array $participantUserIds, int $contextId, bool $sendEmail = true): int
+    {
+        $maxSeq = Query::withAssoc(Application::ASSOC_TYPE_SUBMISSION, $submissionId)
+            ->max('seq') ?? 0;
+
+        $query = Query::create([
+            'assocType' => Application::ASSOC_TYPE_SUBMISSION,
+            'assocId' => $submissionId,
+            'stageId' => $stageId,
+            'seq' => $maxSeq + 1
+        ]);
+
+        $addParticipants = [];
+        foreach (array_unique($participantUserIds) as $participantUserId) {
+            $addParticipants[] = ([
+                'query_id' => $query->id,
+                'user_id' => $participantUserId
+            ]);
+        }
+        QueryParticipant::insert($addParticipants);
+
+        Note::create([
+            'assocType' => Application::ASSOC_TYPE_QUERY,
+            'assocId' => $query->id,
+            'title' =>  $title,
+            'contents' =>  $content,
+            'userId' =>  $fromUser->getId(),
+        ]);
+
+        // Add task for assigned participants
+        $notificationMgr = new NotificationManager();
+
+        /** @var NotificationSubscriptionSettingsDAO */
+        $notificationSubscriptionSettingsDao = DAORegistry::getDAO('NotificationSubscriptionSettingsDAO');
+
+        foreach ($participantUserIds as $participantUserId) {
+            $notificationMgr->createNotification(
+                Application::get()->getRequest(),
+                $participantUserId,
+                Notification::NOTIFICATION_TYPE_NEW_QUERY,
+                $contextId,
+                Application::ASSOC_TYPE_QUERY,
+                $query->id,
+                Notification::NOTIFICATION_LEVEL_TASK
+            );
+
+            if (!$sendEmail) {
+                continue;
+            }
+
+            // Check if the user is unsubscribed
+            $notificationSubscriptionSettings = $notificationSubscriptionSettingsDao->getNotificationSubscriptionSettings(
+                NotificationSubscriptionSettingsDAO::BLOCKED_EMAIL_NOTIFICATION_KEY,
+                $participantUserId,
+                $contextId
+            );
+            if (in_array(Notification::NOTIFICATION_TYPE_NEW_QUERY, $notificationSubscriptionSettings)) {
+                continue;
+            }
+
+            $recipient = Repo::user()->get($participantUserId);
+            $mailable = new Mailable();
+            $mailable->to($recipient->getEmail(), $recipient->getFullName());
+            $mailable->from($fromUser->getEmail(), $fromUser->getFullName());
+            $mailable->subject($title);
+            $mailable->body($content);
+
+            Mail::send($mailable);
+        }
+
+        return $query->id;
+    }
+
+    /**
+     * Create a query with a submission's comments for the editors
+     *
+     * Creates the query and assigns all participants
+     *
+     * @return int new query id
+     */
+    public function addCommentsForEditorsQuery(Submission $submission): int
+    {
+        // Replaces StageAssignmentDAO::getBySubmissionAndRoleIds
+        $participantUserIds = StageAssignment::withSubmissionIds([$submission->getId()])
+            ->withRoleIds([
+                Role::ROLE_ID_MANAGER,
+                Role::ROLE_ID_SUB_EDITOR,
+                Role::ROLE_ID_ASSISTANT,
+                Role::ROLE_ID_AUTHOR,
+            ])
+            ->withStageIds([$submission->getData('stageId')])
+            ->get()
+            ->pluck('user_id')
+            ->all();
+
+        // Replaces StageAssignmentDAO::getBySubmissionAndRoleIds
+        $authorAssignments = StageAssignment::withSubmissionIds([$submission->getId()])
+            ->withRoleIds([Role::ROLE_ID_AUTHOR])
+            ->withStageIds([$submission->getData('stageId')])
+            ->get();
+
+        $fromUser = $authorAssignments->isEmpty()
+            ? Application::get()->getRequest()->getUser()
+            : Repo::user()->get($authorAssignments->first()->userId);
+
+        return $this->addQuery(
+            $submission->getId(),
+            $submission->getData('stageId'),
+            __('submission.submit.coverNote'),
+            $submission->getData('commentsForTheEditors'),
+            $fromUser,
+            $participantUserIds,
+            $submission->getData('contextId')
+        );
+    }
+}
diff --git a/classes/security/authorization/NoteAccessPolicy.php b/classes/security/authorization/NoteAccessPolicy.php
index ee48386fc77..2cfe6f71493 100644
--- a/classes/security/authorization/NoteAccessPolicy.php
+++ b/classes/security/authorization/NoteAccessPolicy.php
@@ -2,8 +2,8 @@
 /**
  * @file classes/security/authorization/NoteAccessPolicy.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class NoteAccessPolicy
@@ -21,7 +21,6 @@
 use APP\core\Application;
 use APP\core\Request;
 use PKP\core\PKPRequest;
-use PKP\db\DAORegistry;
 use PKP\note\Note;
 
 class NoteAccessPolicy extends AuthorizationPolicy
@@ -80,12 +79,12 @@ public function effect()
         }
 
         // Note, query, submission and assigned stages must match
-        if ($note->assocId != $query->getId()
+        if ($note->assocId != $query->id
                 || $note->assocType != Application::ASSOC_TYPE_QUERY
-                || $query->getAssocId() != $submission->getId()
-                || $query->getAssocType() != Application::ASSOC_TYPE_SUBMISSION
-                || !array_key_exists($query->getStageId(), $assignedStages)
-                || empty($assignedStages[$query->getStageId()])) {
+                || $query->assocId != $submission->getId()
+                || $query->assocType != Application::ASSOC_TYPE_SUBMISSION
+                || !array_key_exists($query->stageId, $assignedStages)
+                || empty($assignedStages[$query->stageId])) {
             return AuthorizationPolicy::AUTHORIZATION_DENY;
         }
 
diff --git a/classes/security/authorization/internal/QueryAssignedToUserAccessPolicy.php b/classes/security/authorization/internal/QueryAssignedToUserAccessPolicy.php
index a5b7e969f58..ad2ef8521ba 100644
--- a/classes/security/authorization/internal/QueryAssignedToUserAccessPolicy.php
+++ b/classes/security/authorization/internal/QueryAssignedToUserAccessPolicy.php
@@ -2,8 +2,8 @@
 /**
  * @file classes/security/authorization/internal/QueryAssignedToUserAccessPolicy.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class QueryAssignedToUserAccessPolicy
@@ -18,10 +18,11 @@
 
 use APP\core\Application;
 use PKP\core\PKPRequest;
-use PKP\db\DAORegistry;
-use PKP\query\QueryDAO;
+use PKP\query\Query;
+use PKP\query\QueryParticipant;
 use PKP\security\authorization\AuthorizationPolicy;
 use PKP\security\Role;
+use PKP\user\User;
 
 class QueryAssignedToUserAccessPolicy extends AuthorizationPolicy
 {
@@ -49,26 +50,28 @@ public function effect()
     {
         // A query should already be in the context.
         $query = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_QUERY);
-        if (!$query instanceof \PKP\query\Query) {
+        if (!$query instanceof Query) {
             return AuthorizationPolicy::AUTHORIZATION_DENY;
         }
 
         // Check that there is a currently logged in user.
         $user = $this->_request->getUser();
-        if (!$user instanceof \PKP\user\User) {
+        if (!$user instanceof User) {
             return AuthorizationPolicy::AUTHORIZATION_DENY;
         }
 
         // Determine if the query is assigned to the user.
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        if ($queryDao->getParticipantIds($query->getId(), $user->getId())) {
+        $participantIds = QueryParticipant::withQueryId($query->id)
+            ->pluck('user_id')
+            ->all();
+        if (in_array($user->getId(), $participantIds)) {
             return AuthorizationPolicy::AUTHORIZATION_PERMIT;
         }
 
         // Managers are allowed to access discussions they are not participants in
         // as long as they have Manager-level access to the workflow stage
         $accessibleWorkflowStages = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_ACCESSIBLE_WORKFLOW_STAGES);
-        $managerAssignments = array_intersect([Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN], $accessibleWorkflowStages[$query->getStageId()] ?? []);
+        $managerAssignments = array_intersect([Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN], $accessibleWorkflowStages[$query->stageId] ?? []);
         if (!empty($managerAssignments)) {
             return AuthorizationPolicy::AUTHORIZATION_PERMIT;
         }
@@ -77,7 +80,3 @@ public function effect()
         return AuthorizationPolicy::AUTHORIZATION_DENY;
     }
 }
-
-if (!PKP_STRICT_MODE) {
-    class_alias('\PKP\security\authorization\internal\QueryAssignedToUserAccessPolicy', '\QueryAssignedToUserAccessPolicy');
-}
diff --git a/classes/security/authorization/internal/QueryRequiredPolicy.php b/classes/security/authorization/internal/QueryRequiredPolicy.php
index c17b31e4975..ae5f63a74c1 100644
--- a/classes/security/authorization/internal/QueryRequiredPolicy.php
+++ b/classes/security/authorization/internal/QueryRequiredPolicy.php
@@ -2,8 +2,8 @@
 /**
  * @file classes/security/authorization/internal/QueryRequiredPolicy.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class QueryRequiredPolicy
@@ -18,9 +18,7 @@
 use APP\core\Application;
 use APP\submission\Submission;
 use PKP\core\PKPRequest;
-use PKP\db\DAORegistry;
 use PKP\query\Query;
-use PKP\query\QueryDAO;
 use PKP\security\authorization\AuthorizationPolicy;
 use PKP\security\authorization\DataObjectRequiredPolicy;
 
@@ -52,18 +50,17 @@ public function dataObjectEffect()
         }
 
         // Make sure the query belongs to the submission.
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $query = $queryDao->getById($queryId);
+        $query = Query::find($queryId);
         if (!$query instanceof Query) {
             return AuthorizationPolicy::AUTHORIZATION_DENY;
         }
-        switch ($query->getAssocType()) {
+        switch ($query->assocType) {
             case Application::ASSOC_TYPE_SUBMISSION:
                 $submission = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_SUBMISSION);
                 if (!$submission instanceof Submission) {
                     return AuthorizationPolicy::AUTHORIZATION_DENY;
                 }
-                if ($query->getAssocId() != $submission->getId()) {
+                if ($query->assocId != $submission->getId()) {
                     return AuthorizationPolicy::AUTHORIZATION_DENY;
                 }
                 break;
@@ -76,7 +73,3 @@ public function dataObjectEffect()
         return AuthorizationPolicy::AUTHORIZATION_PERMIT;
     }
 }
-
-if (!PKP_STRICT_MODE) {
-    class_alias('\PKP\security\authorization\internal\QueryRequiredPolicy', '\QueryRequiredPolicy');
-}
diff --git a/classes/security/authorization/internal/SubmissionFileAssignedQueryAccessPolicy.php b/classes/security/authorization/internal/SubmissionFileAssignedQueryAccessPolicy.php
index 9c6107704d2..65b7e603c71 100644
--- a/classes/security/authorization/internal/SubmissionFileAssignedQueryAccessPolicy.php
+++ b/classes/security/authorization/internal/SubmissionFileAssignedQueryAccessPolicy.php
@@ -2,8 +2,8 @@
 /**
  * @file classes/security/authorization/internal/SubmissionFileAssignedQueryAccessPolicy.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class SubmissionFileAssignedQueryAccessPolicy
@@ -18,10 +18,12 @@
 namespace PKP\security\authorization\internal;
 
 use APP\core\Application;
-use PKP\db\DAORegistry;
 use PKP\note\Note;
-use PKP\query\QueryDAO;
+use PKP\query\Query;
+use PKP\query\QueryParticipant;
 use PKP\security\authorization\AuthorizationPolicy;
+use PKP\submissionFile\SubmissionFile;
+use PKP\user\User;
 
 class SubmissionFileAssignedQueryAccessPolicy extends SubmissionFileBaseAccessPolicy
 {
@@ -37,13 +39,13 @@ public function effect()
 
         // Get the user
         $user = $request->getUser();
-        if (!$user instanceof \PKP\user\User) {
+        if (!$user instanceof User) {
             return AuthorizationPolicy::AUTHORIZATION_DENY;
         }
 
         // Get the submission file
         $submissionFile = $this->getSubmissionFile($request);
-        if (!$submissionFile instanceof \PKP\submissionFile\SubmissionFile) {
+        if (!$submissionFile instanceof SubmissionFile) {
             return AuthorizationPolicy::AUTHORIZATION_DENY;
         }
 
@@ -53,27 +55,25 @@ public function effect()
         }
 
         $note = Note::find($submissionFile->getData('assocId'));
-        if (!$note instanceof \PKP\note\Note) {
+        if (!$note instanceof Note) {
             return AuthorizationPolicy::AUTHORIZATION_DENY;
         }
 
         if ($note->assocType != Application::ASSOC_TYPE_QUERY) {
             return AuthorizationPolicy::AUTHORIZATION_DENY;
         }
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $query = $queryDao->getById($note->assocId);
+        $query = Query::find($note->assocId);
         if (!$query) {
             return AuthorizationPolicy::AUTHORIZATION_DENY;
         }
 
-        if ($queryDao->getParticipantIds($note->assocId, $user->getId())) {
+        $participantIds = QueryParticipant::withQueryId($query->id)
+            ->pluck('user_id')
+            ->all();
+        if (in_array($user->getId(), $participantIds)) {
             return AuthorizationPolicy::AUTHORIZATION_PERMIT;
         }
 
         return AuthorizationPolicy::AUTHORIZATION_DENY;
     }
 }
-
-if (!PKP_STRICT_MODE) {
-    class_alias('\PKP\security\authorization\internal\SubmissionFileAssignedQueryAccessPolicy', '\SubmissionFileAssignedQueryAccessPolicy');
-}
diff --git a/classes/submission/DAO.php b/classes/submission/DAO.php
index ed370621dd5..0f77269aa05 100644
--- a/classes/submission/DAO.php
+++ b/classes/submission/DAO.php
@@ -2,8 +2,8 @@
 /**
  * @file classes/submission/DAO.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class DAO
@@ -27,7 +27,7 @@
 use PKP\log\event\EventLogEntry;
 use PKP\note\Note;
 use PKP\notification\Notification;
-use PKP\query\QueryDAO;
+use PKP\query\Query;
 use PKP\services\PKPSchemaService;
 use PKP\stageAssignment\StageAssignment;
 use PKP\submission\reviewRound\ReviewRoundDAO;
@@ -278,8 +278,8 @@ public function deleteById(int $id): int
         $reviewRoundDao->deleteBySubmissionId($id);
 
         // Delete the queries associated with a submission
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $queryDao->deleteByAssoc(Application::ASSOC_TYPE_SUBMISSION, $id);
+        Query::withAssoc(Application::ASSOC_TYPE_SUBMISSION, $id)
+            ->delete();
 
         // Delete the stage assignments.
         StageAssignment::withSubmissionIds([$id])
diff --git a/classes/submission/Repository.php b/classes/submission/Repository.php
index ea6e9496c99..78b5e638fac 100644
--- a/classes/submission/Repository.php
+++ b/classes/submission/Repository.php
@@ -2,8 +2,8 @@
 /**
  * @file classes/submission/Repository.php
  *
- * Copyright (c) 2014-2020 Simon Fraser University
- * Copyright (c) 2000-2020 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class Repository
@@ -32,7 +32,6 @@
 use PKP\facades\Locale;
 use PKP\observers\events\SubmissionSubmitted;
 use PKP\plugins\Hook;
-use PKP\query\QueryDAO;
 use PKP\security\Role;
 use PKP\security\RoleDAO;
 use PKP\services\PKPSchemaService;
@@ -614,9 +613,7 @@ public function submit(Submission $submission, Context $context): void
         );
 
         if ($submission->getData('commentsForTheEditors')) {
-            /** @var QueryDAO $queryDao */
-            $queryDao = DAORegistry::getDAO('QueryDAO');
-            $queryDao->addCommentsForEditorsQuery($submission);
+            Repo::query()->addCommentsForEditorsQuery($submission);
         }
     }
 
diff --git a/classes/submission/maps/Schema.php b/classes/submission/maps/Schema.php
index c02e101eae9..55eea5ba5b2 100644
--- a/classes/submission/maps/Schema.php
+++ b/classes/submission/maps/Schema.php
@@ -2,8 +2,8 @@
 /**
  * @file classes/submission/maps/Schema.php
  *
- * Copyright (c) 2014-2020 Simon Fraser University
- * Copyright (c) 2000-2020 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class Schema
@@ -22,7 +22,7 @@
 use PKP\db\DAORegistry;
 use PKP\plugins\Hook;
 use PKP\plugins\PluginRegistry;
-use PKP\query\QueryDAO;
+use PKP\query\Query;
 use PKP\security\Role;
 use PKP\services\PKPSchemaService;
 use PKP\stageAssignment\StageAssignment;
@@ -511,8 +511,7 @@ public function getPropertyStages(Submission $submission): array
         $request = Application::get()->getRequest();
         $currentUser = $request->getUser();
 
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $openPerStage = $queryDao->countOpenPerStage($submission->getId(), [$request->getUser()->getId()]);
+        $openPerStage = Repo::query()->countOpenPerStage($submission->getId(), [$request->getUser()->getId()]);
 
         $stages = [];
         foreach ($stageIds as $stageId) {
diff --git a/classes/submissionFile/Repository.php b/classes/submissionFile/Repository.php
index 7a6483607b1..5d859a0afc9 100644
--- a/classes/submissionFile/Repository.php
+++ b/classes/submissionFile/Repository.php
@@ -2,8 +2,8 @@
 /**
  * @file classes/submissionFile/Repository.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class Repository
@@ -33,7 +33,7 @@
 use PKP\note\Note;
 use PKP\notification\Notification;
 use PKP\plugins\Hook;
-use PKP\query\QueryDAO;
+use PKP\query\Query;
 use PKP\security\authorization\SubmissionFileAccessPolicy;
 use PKP\security\Role;
 use PKP\security\Validation;
@@ -706,11 +706,10 @@ public function getWorkflowStageId(SubmissionFile $submissionFile): ?int
             }
 
             // Get the associated query.
-            $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-            $query = $queryDao->getById($note->assocId);
+            $query = Query::find($note->assocId);
 
             // The query will have an associated file stage.
-            return $query?->getStageId();
+            return $query?->stageId;
         }
 
         throw new Exception('Could not determine the workflow stage id from submission file ' . $submissionFile->getId() . ' with file stage ' . $submissionFile->getData('fileStage'));
diff --git a/controllers/grid/files/SubmissionFilesCategoryGridDataProvider.php b/controllers/grid/files/SubmissionFilesCategoryGridDataProvider.php
index b71b034c40d..8858f5e2104 100644
--- a/controllers/grid/files/SubmissionFilesCategoryGridDataProvider.php
+++ b/controllers/grid/files/SubmissionFilesCategoryGridDataProvider.php
@@ -3,8 +3,8 @@
 /**
  * @file controllers/grid/files/SubmissionFilesCategoryGridDataProvider.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class SubmissionFilesCategoryGridDataProvider
@@ -21,7 +21,7 @@
 use PKP\controllers\grid\CategoryGridDataProvider;
 use PKP\db\DAORegistry;
 use PKP\note\Note;
-use PKP\query\QueryDAO;
+use PKP\query\Query;
 use PKP\submission\reviewRound\ReviewRoundDAO;
 use PKP\submissionFile\SubmissionFile;
 
@@ -149,11 +149,10 @@ public function loadCategoryData($request, $categoryDataElement, $filter = null,
                         break;
                     }
                     $note = Note::find($submissionFile->getData('assocId'));
-                    $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
                     if ($note?->assocType == Application::ASSOC_TYPE_QUERY) {
-                        $query = $queryDao->getById($note->assocId);
+                        $query = Query::find($note->assocId);
                     }
-                    if ($query && $query->getStageId() == $stageId) {
+                    if ($query && $query->stageId == $stageId) {
                         $stageSubmissionFiles[$key] = $submissionFile;
                     }
                 }
diff --git a/controllers/grid/files/query/ManageQueryNoteFilesGridHandler.php b/controllers/grid/files/query/ManageQueryNoteFilesGridHandler.php
index f914bab2fd2..6d63533958f 100644
--- a/controllers/grid/files/query/ManageQueryNoteFilesGridHandler.php
+++ b/controllers/grid/files/query/ManageQueryNoteFilesGridHandler.php
@@ -3,8 +3,8 @@
 /**
  * @file controllers/grid/files/query/ManageQueryNoteFilesGridHandler.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2003-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2003-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class ManageQueryNoteFilesGridHandler
@@ -17,6 +17,7 @@
 namespace PKP\controllers\grid\files\query;
 
 use APP\core\Application;
+use APP\facades\Repo;
 use PKP\controllers\grid\files\FilesGridCapabilities;
 use PKP\controllers\grid\files\query\form\ManageQueryNoteFilesForm;
 use PKP\controllers\grid\files\SelectableSubmissionFileListCategoryGridHandler;
@@ -78,7 +79,7 @@ public function isDataElementInCategorySelected($categoryDataId, &$gridDataEleme
 
         // Passed the checks above. If it's part of the current query, mark selected.
         $query = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_QUERY);
-        $headNote = $query->getHeadNote();
+        $headNote = Repo::note()->getHeadNote($query->id);
         return $submissionFile->getData('assocType') == Application::ASSOC_TYPE_NOTE && $submissionFile->getData('assocId') == $headNote->id;
     }
 
@@ -98,7 +99,7 @@ public function updateQueryNoteFiles($args, $request)
         $submission = $this->getSubmission();
         $query = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_QUERY);
 
-        $manageQueryNoteFilesForm = new ManageQueryNoteFilesForm($submission->getId(), $query->getId(), $request->getUserVar('noteId'));
+        $manageQueryNoteFilesForm = new ManageQueryNoteFilesForm($submission->getId(), $query->id, $request->getUserVar('noteId'));
         $manageQueryNoteFilesForm->readInputData();
 
         if ($manageQueryNoteFilesForm->validate()) {
diff --git a/controllers/grid/files/query/QueryNoteFilesGridDataProvider.php b/controllers/grid/files/query/QueryNoteFilesGridDataProvider.php
index afcf6518028..db37f65e737 100644
--- a/controllers/grid/files/query/QueryNoteFilesGridDataProvider.php
+++ b/controllers/grid/files/query/QueryNoteFilesGridDataProvider.php
@@ -3,8 +3,8 @@
 /**
  * @file controllers/grid/files/query/QueryNoteFilesGridDataProvider.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2003-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2003-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class QueryNoteFilesGridDataProvider
@@ -22,7 +22,6 @@
 use PKP\controllers\api\file\linkAction\AddFileLinkAction;
 use PKP\controllers\grid\files\fileList\linkAction\SelectFilesLinkAction;
 use PKP\controllers\grid\files\SubmissionFilesGridDataProvider;
-use PKP\db\DAORegistry;
 use PKP\note\Note;
 use PKP\security\authorization\QueryAccessPolicy;
 use PKP\submissionFile\SubmissionFile;
@@ -79,7 +78,7 @@ public function loadData($filter = [])
         $query = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_QUERY);
 
         $note = Note::find($this->_noteId);
-        if ($note->assocType != Application::ASSOC_TYPE_QUERY || $note->assocId != $query->getId()) {
+        if ($note->assocType != Application::ASSOC_TYPE_QUERY || $note->assocId != $query->id) {
             throw new Exception('Invalid note ID specified!');
         }
 
@@ -107,7 +106,7 @@ public function getRequestArgs()
             [
                 'assocType' => Application::ASSOC_TYPE_NOTE,
                 'assocId' => $this->_noteId,
-                'queryId' => $query->getId(),
+                'queryId' => $query->id,
                 'noteId' => $this->_noteId,
                 'representationId' => $representation ? $representation->getId() : null,
             ]
@@ -132,7 +131,7 @@ public function getAddFileAction($request)
             null,
             null,
             false,
-            $query->getId()
+            $query->id
         );
     }
 }
diff --git a/controllers/grid/files/query/QueryNoteFilesGridHandler.php b/controllers/grid/files/query/QueryNoteFilesGridHandler.php
index ee6ed0ac5ad..a1267f2b399 100644
--- a/controllers/grid/files/query/QueryNoteFilesGridHandler.php
+++ b/controllers/grid/files/query/QueryNoteFilesGridHandler.php
@@ -3,8 +3,8 @@
 /**
  * @file controllers/grid/files/query/QueryNoteFilesGridHandler.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2003-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2003-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class QueryNoteFilesGridHandler
@@ -91,7 +91,7 @@ public function selectFiles($args, $request)
         $submission = $this->getSubmission();
         $query = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_QUERY);
 
-        $manageQueryNoteFilesForm = new ManageQueryNoteFilesForm($submission->getId(), $query->getId(), $request->getUserVar('noteId'), $this->getRequestArgs());
+        $manageQueryNoteFilesForm = new ManageQueryNoteFilesForm($submission->getId(), $query->id, $request->getUserVar('noteId'), $this->getRequestArgs());
         $manageQueryNoteFilesForm->initData();
         return new JSONMessage(true, $manageQueryNoteFilesForm->fetch($request));
     }
diff --git a/controllers/grid/notifications/NotificationsGridCellProvider.php b/controllers/grid/notifications/NotificationsGridCellProvider.php
index 10abe25a3cc..bbe1e393fc5 100644
--- a/controllers/grid/notifications/NotificationsGridCellProvider.php
+++ b/controllers/grid/notifications/NotificationsGridCellProvider.php
@@ -3,8 +3,8 @@
 /**
  * @file controllers/grid/notifications/NotificationsGridCellProvider.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class NotificationsGridCellProvider
@@ -29,7 +29,7 @@
 use PKP\linkAction\request\AjaxAction;
 use PKP\notification\Notification;
 use PKP\payment\QueuedPaymentDAO;
-use PKP\query\QueryDAO;
+use PKP\query\Query;
 use PKP\submission\reviewRound\ReviewRoundDAO;
 
 class NotificationsGridCellProvider extends GridCellProvider
@@ -152,16 +152,15 @@ public function _getTitle($notification)
                 $submissionId = $reviewRound->getSubmissionId();
                 break;
             case Application::ASSOC_TYPE_QUERY:
-                $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-                $query = $queryDao->getById($notification->assocId);
+                $query = Query::find($notification->assocId);
                 assert($query instanceof \PKP\query\Query);
-                switch ($query->getAssocType()) {
+                switch ($query->assocType) {
                     case Application::ASSOC_TYPE_SUBMISSION:
-                        $submissionId = $query->getAssocId();
+                        $submissionId = $query->assocId;
                         break;
                     case Application::ASSOC_TYPE_REPRESENTATION:
                         $representationDao = Application::getRepresentationDAO();
-                        $representation = $representationDao->getById($query->getAssocId());
+                        $representation = $representationDao->getById($query->assocId);
                         $publication = Repo::publication()->get($representation->getData('publicationId'));
                         $submissionId = $publication->getData('submissionId');
                         break;
diff --git a/controllers/grid/queries/QueriesAccessHelper.php b/controllers/grid/queries/QueriesAccessHelper.php
index d1f02b74cf5..0946fe54a17 100644
--- a/controllers/grid/queries/QueriesAccessHelper.php
+++ b/controllers/grid/queries/QueriesAccessHelper.php
@@ -27,9 +27,9 @@
 namespace PKP\controllers\grid\queries;
 
 use APP\core\Application;
-use PKP\db\DAORegistry;
+use APP\facades\Repo;
 use PKP\query\Query;
-use PKP\query\QueryDAO;
+use PKP\query\QueryParticipant;
 use PKP\security\Role;
 use PKP\user\User;
 
@@ -73,12 +73,12 @@ public function getAuthorizedContextObject($assocType)
     public function getCanOpenClose($query)
     {
         // Managers and sub editors are always allowed
-        if ($this->hasStageRole($query->getStageId(), [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN, Role::ROLE_ID_SUB_EDITOR])) {
+        if ($this->hasStageRole($query->stageId, [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN, Role::ROLE_ID_SUB_EDITOR])) {
             return true;
         }
 
         // Assigned assistants are allowed
-        if ($this->hasStageRole($query->getStageId(), [Role::ROLE_ID_ASSISTANT]) && $this->isAssigned($this->_user->getId(), $query->getId())) {
+        if ($this->hasStageRole($query->stageId, [Role::ROLE_ID_ASSISTANT]) && $this->isAssigned($this->_user->getId(), $query->id)) {
             return true;
         }
 
@@ -119,22 +119,21 @@ public function getCanCreate($stageId)
      */
     public function getCanEdit($queryId)
     {
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $query = $queryDao->getById($queryId);
+        $query = Query::find($queryId);
         if (!$query) {
             return false;
         }
 
         // Assistants, authors and reviewers are allowed, if they created the query less than x seconds ago
-        if ($this->hasStageRole($query->getStageId(), [Role::ROLE_ID_ASSISTANT, Role::ROLE_ID_AUTHOR, Role::ROLE_ID_REVIEWER])) {
-            $headNote = $query->getHeadNote();
+        if ($this->hasStageRole($query->stageId, [Role::ROLE_ID_ASSISTANT, Role::ROLE_ID_AUTHOR, Role::ROLE_ID_REVIEWER])) {
+            $headNote = Repo::note()->getHeadNote($query->id);
             if ($headNote->userId == $this->_user->getId() && ($headNote->dateCreated->diffInHours() < 1)) {
                 return true;
             }
         }
 
         // Managers are always allowed
-        if ($this->hasStageRole($query->getStageId(), [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN, Role::ROLE_ID_SUB_EDITOR])) {
+        if ($this->hasStageRole($query->stageId, [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN, Role::ROLE_ID_SUB_EDITOR])) {
             return true;
         }
 
@@ -152,17 +151,16 @@ public function getCanEdit($queryId)
     public function getCanDelete($queryId)
     {
         // Users can always delete their own placeholder queries.
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $query = $queryDao->getById($queryId);
+        $query = Query::find($queryId);
         if ($query) {
-            $headNote = $query->getHeadNote();
+            $headNote = Repo::note()->getHeadNote($query->id);
             if ($headNote?->userId == $this->_user->getId() && $headNote?->title == '') {
                 return true;
             }
         }
 
         // Managers and site admins are always allowed
-        if ($this->hasStageRole($query->getStageId(), [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN])) {
+        if ($this->hasStageRole($query->stageId, [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN])) {
             return true;
         }
 
@@ -193,8 +191,10 @@ public function getCanListAll($stageId)
      */
     protected function isAssigned($userId, $queryId)
     {
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        return (bool) $queryDao->getParticipantIds($queryId, $userId);
+        $participantIds = QueryParticipant::withQueryId($queryId)
+            ->pluck('user_id')
+            ->all();
+        return in_array($userId, $participantIds);
     }
 
     /**
diff --git a/controllers/grid/queries/QueriesGridCellProvider.php b/controllers/grid/queries/QueriesGridCellProvider.php
index 60226aca263..71f74b21400 100644
--- a/controllers/grid/queries/QueriesGridCellProvider.php
+++ b/controllers/grid/queries/QueriesGridCellProvider.php
@@ -17,6 +17,7 @@
 namespace PKP\controllers\grid\queries;
 
 use APP\core\Application;
+use APP\facades\Repo;
 use APP\submission\Submission;
 use Illuminate\Database\Eloquent\Model;
 use PKP\controllers\grid\DataObjectGridCellProvider;
@@ -75,9 +76,9 @@ public function getTemplateVarsFromRowColumn($row, $column)
         $columnId = $column->getId();
         assert(($element instanceof DataObject || $element instanceof Model) && !empty($columnId));
         /** @var Query $element */
-        $headNote = $element->getHeadNote();
+        $headNote = Repo::note()->getHeadNote($element->id);
         $user = $headNote?->user;
-        $notes = Note::withAssoc(PKPApplication::ASSOC_TYPE_QUERY, $element->getId())
+        $notes = Note::withAssoc(PKPApplication::ASSOC_TYPE_QUERY, $element->id)
             ->withSort(Note::NOTE_ORDER_ID)
             ->lazy();
         $context = Application::get()->getRequest()->getContext();
@@ -87,19 +88,19 @@ public function getTemplateVarsFromRowColumn($row, $column)
             case 'replies':
                 return ['label' => max(0, $notes->count() - 1)];
             case 'from':
-                return ['label' => ($user?->getUsername() ?? '&mdash;') . '<br />' . $headNote?->dateCreated?->locale(Locale::getLocale())?->translatedFormat($datetimeFormatShort)];
+                return ['label' => ($user?->getUsername() ?? '&mdash;') . '<br />' . $headNote?->dateCreated->format($datetimeFormatShort)];
             case 'lastReply':
                 $latestReply = $notes->first();
-                if ($latestReply && $latestReply->getId() != $headNote->id) {
+                if ($latestReply && $latestReply->id != $headNote->id) {
                     $repliedUser = $latestReply->user;
-                    return ['label' => ($repliedUser?->getUsername() ?? '&mdash;') . '<br />' . $latestReply->dateCreated->locale(Locale::getLocale())->translatedFormat($datetimeFormatShort)];
+                    return ['label' => ($repliedUser?->getUsername() ?? '&mdash;') . '<br />' . $latestReply->dateCreated->format($datetimeFormatShort)];
                 } else {
                     return ['label' => '-'];
                 }
                 // no break
             case 'closed':
                 return [
-                    'selected' => $element->getIsClosed(),
+                    'selected' => $element->closed,
                     'disabled' => !$this->_queriesAccessHelper->getCanOpenClose($element),
                 ];
         }
@@ -117,7 +118,7 @@ public function getCellActions($request, $row, $column, $position = GridHandler:
         switch ($column->getId()) {
             case 'closed':
                 if ($this->_queriesAccessHelper->getCanOpenClose($element)) {
-                    $enabled = !$element->getIsClosed();
+                    $enabled = !$element->closed;
                     if ($enabled) {
                         return [new LinkAction(
                             'close-' . $row->getId(),
diff --git a/controllers/grid/queries/QueriesGridHandler.php b/controllers/grid/queries/QueriesGridHandler.php
index caedd3b2524..c7c8bb55efe 100644
--- a/controllers/grid/queries/QueriesGridHandler.php
+++ b/controllers/grid/queries/QueriesGridHandler.php
@@ -3,8 +3,8 @@
 /**
  * @file controllers/grid/queries/QueriesGridHandler.php
  *
- * Copyright (c) 2016-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * Copyright (c) 2016-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class QueriesGridHandler
@@ -30,15 +30,17 @@
 use PKP\core\JSONMessage;
 use PKP\core\PKPApplication;
 use PKP\core\PKPRequest;
+use PKP\db\DAO;
 use PKP\db\DAORegistry;
 use PKP\linkAction\LinkAction;
 use PKP\linkAction\request\AjaxModal;
 use PKP\linkAction\request\RemoteActionConfirmationModal;
 use PKP\log\SubmissionEmailLogEventType;
+use PKP\note\Note;
 use PKP\notification\Notification;
 use PKP\notification\NotificationSubscriptionSettingsDAO;
 use PKP\query\Query;
-use PKP\query\QueryDAO;
+use PKP\query\QueryParticipant;
 use PKP\security\authorization\QueryAccessPolicy;
 use PKP\security\authorization\QueryWorkflowStageAccessPolicy;
 use PKP\security\Role;
@@ -264,7 +266,7 @@ public function initFeatures($request, $args)
      */
     public function getDataElementSequence($row)
     {
-        return $row->getSequence();
+        return $row->seq;
     }
 
     /**
@@ -272,10 +274,9 @@ public function getDataElementSequence($row)
      */
     public function setDataElementSequence($request, $rowId, $gridDataElement, $newSequence)
     {
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $query = $queryDao->getById($rowId, $this->getAssocType(), $this->getAssocId());
-        $query->setSequence($newSequence);
-        $queryDao->updateObject($query);
+        $query = Query::where('id', $rowId)->withAssoc($this->getAssocType(), $this->getAssocId())->first();
+        $query->seq = $newSequence;
+        $query->save();
     }
 
     /**
@@ -323,13 +324,12 @@ public function getRequestArgs()
      */
     public function loadData($request, $filter = null)
     {
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        return $queryDao->getByAssoc(
-            $this->getAssocType(),
-            $this->getAssocId(),
-            $this->getStageId(),
-            $this->getAccessHelper()->getCanListAll($this->getStageId()) ? null : $request->getUser()->getId()
-        );
+        $user = $this->getAccessHelper()->getCanListAll($this->getStageId()) ? null : $request->getUser()->getId();
+
+        return Query::withAssoc($this->getAssocType(), $this->getAssocId())
+            ->withStageId($this->getStageId())
+            ->when($user, fn ($q) => $q->withUserId($user))
+            ->lazy();
     }
 
     //
@@ -370,14 +370,13 @@ public function addQuery($args, $request)
     public function deleteQuery($args, $request)
     {
         $query = $this->getQuery();
-        if (!$request->checkCSRF() || !$query || !$this->getAccessHelper()->getCanDelete($query->getId())) {
+        if (!$request->checkCSRF() || !$query || !$this->getAccessHelper()->getCanDelete($query->id)) {
             return new JSONMessage(false);
         }
 
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $queryDao->deleteObject($query);
-
-        Notification::withAssoc(PKPApplication::ASSOC_TYPE_QUERY, $query->getId())->delete();
+        $query->delete();
+        Note::withAssoc(PKPApplication::ASSOC_TYPE_QUERY, $query->id)->delete();
+        Notification::withAssoc(PKPApplication::ASSOC_TYPE_QUERY, $query->id)->delete();
 
         if ($this->getStageId() == WORKFLOW_STAGE_ID_EDITING ||
             $this->getStageId() == WORKFLOW_STAGE_ID_PRODUCTION) {
@@ -397,7 +396,7 @@ public function deleteQuery($args, $request)
             );
         }
 
-        return \PKP\db\DAO::getDataChangedEvent($query->getId());
+        return DAO::getDataChangedEvent($query->id);
     }
 
     /**
@@ -415,10 +414,9 @@ public function openQuery($args, $request)
             return new JSONMessage(false);
         }
 
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $query->setIsClosed(false);
-        $queryDao->updateObject($query);
-        return \PKP\db\DAO::getDataChangedEvent($query->getId());
+        $query->closed = false;
+        $query->save();
+        return DAO::getDataChangedEvent($query->id);
     }
 
     /**
@@ -436,10 +434,9 @@ public function closeQuery($args, $request)
             return new JSONMessage(false);
         }
 
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $query->setIsClosed(true);
-        $queryDao->updateObject($query);
-        return \PKP\db\DAO::getDataChangedEvent($query->getId());
+        $query->closed = true;
+        $query->save();
+        return DAO::getDataChangedEvent($query->id);
     }
 
     /**
@@ -467,10 +464,10 @@ public function readQuery($args, $request)
         $user = $request->getUser();
         $context = $request->getContext();
 
-        $actionArgs = array_merge($this->getRequestArgs(), ['queryId' => $query->getId()]);
+        $actionArgs = array_merge($this->getRequestArgs(), ['queryId' => $query->id]);
 
         // If appropriate, create an Edit action for the participants list
-        if ($this->getAccessHelper()->getCanEdit($query->getId())) {
+        if ($this->getAccessHelper()->getCanEdit($query->id)) {
             $editAction = new LinkAction(
                 'editQuery',
                 new AjaxModal(
@@ -499,7 +496,7 @@ public function readQuery($args, $request)
         );
 
         // Show leave query button for journal managers included in the query
-        if ($user && $this->_getCurrentUserCanLeave($query->getId())) {
+        if ($user && $this->_getCurrentUserCanLeave($query->id)) {
             $showLeaveQueryButton = true;
         } else {
             $showLeaveQueryButton = false;
@@ -528,22 +525,20 @@ public function readQuery($args, $request)
     public function participants($args, $request)
     {
         $query = $this->getQuery();
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $context = $request->getContext();
         $user = $request->getUser();
 
         $participants = [];
-        foreach ($queryDao->getParticipantIds($query->getId()) as $userId) {
-            $user = Repo::user()->get($userId);
-            if ($user) {
-                $participants[] = $user;
+        $queryParticipants = $query->queryParticipants;
+        foreach ($queryParticipants as $participant) {
+            if ($participant->user) {
+                $participants[] = $participant->user;
             }
         }
 
         $templateMgr = TemplateManager::getManager($request);
         $templateMgr->assign('participants', $participants);
 
-        if ($user && $this->_getCurrentUserCanLeave($query->getId())) {
+        if ($user && $this->_getCurrentUserCanLeave($query->id)) {
             $showLeaveQueryButton = true;
         } else {
             $showLeaveQueryButton = false;
@@ -566,7 +561,7 @@ public function participants($args, $request)
     public function editQuery($args, $request)
     {
         $query = $this->getQuery();
-        if (!$this->getAccessHelper()->getCanEdit($query->getId())) {
+        if (!$this->getAccessHelper()->getCanEdit($query->id)) {
             return new JSONMessage(false);
         }
 
@@ -576,7 +571,7 @@ public function editQuery($args, $request)
             $this->getAssocType(),
             $this->getAssocId(),
             $this->getStageId(),
-            $query->getId()
+            $query->id
         );
         $queryForm->initData();
         return new JSONMessage(true, $queryForm->fetch($request, null, false, $this->getRequestArgs()));
@@ -593,19 +588,19 @@ public function editQuery($args, $request)
     public function updateQuery($args, $request)
     {
         $query = $this->getQuery();
-        if (!$this->getAccessHelper()->getCanEdit($query->getId())) {
+        if (!$this->getAccessHelper()->getCanEdit($query->id)) {
             return new JSONMessage(false);
         }
-        /** @var QueryDAO */
-        $queryDao = DAORegistry::getDAO('QueryDAO');
-        $oldParticipantIds = $queryDao->getParticipantIds($query->getId());
+        $oldParticipantIds = QueryParticipant::withQueryId($query->id)
+            ->pluck('user_id')
+            ->all();
 
         $queryForm = new QueryForm(
             $request,
             $this->getAssocType(),
             $this->getAssocId(),
             $this->getStageId(),
-            $query->getId()
+            $query->id
         );
         $queryForm->readInputData();
 
@@ -641,7 +636,7 @@ public function updateQuery($args, $request)
 
             /** @var NotificationSubscriptionSettingsDAO */
             $notificationSubscriptionSettingsDao = DAORegistry::getDAO('NotificationSubscriptionSettingsDAO');
-            $note = $query->getHeadNote();
+            $note = Repo::note()->getHeadNote($query->id);
             $submission = $this->getSubmission();
 
             // Find attachments if any
@@ -662,7 +657,7 @@ public function updateQuery($args, $request)
                     Notification::NOTIFICATION_TYPE_NEW_QUERY,
                     $request->getContext()->getId(),
                     PKPApplication::ASSOC_TYPE_QUERY,
-                    $query->getId(),
+                    $query->id,
                     Notification::NOTIFICATION_LEVEL_TASK
                 );
 
@@ -692,7 +687,7 @@ public function updateQuery($args, $request)
                 Repo::emailLogEntry()->logMailable(SubmissionEmailLogEventType::DISCUSSION_NOTIFY, $mailable, $submission);
             }
 
-            return \PKP\db\DAO::getDataChangedEvent($query->getId());
+            return DAO::getDataChangedEvent($query->id);
         }
 
         // If this was new (placeholder) query that didn't validate, remember whether or not
@@ -708,7 +703,7 @@ public function updateQuery($args, $request)
                 false,
                 array_merge(
                     $this->getRequestArgs(),
-                    ['queryId' => $query->getId()]
+                    ['queryId' => $query->id]
                 )
             )
         );
@@ -727,8 +722,9 @@ public function leaveQuery($args, $request)
         $queryId = $args['queryId'];
         $user = $request->getUser();
         if ($user && $this->_getCurrentUserCanLeave($queryId)) {
-            $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-            $queryDao->removeParticipant($queryId, $user->getId());
+            QueryParticipant::withQueryId($queryId)
+                ->withUserId($user->getId())
+                ->delete();
             $json = new JSONMessage();
             $json->setEvent('user-left-discussion');
         } else {
@@ -750,8 +746,9 @@ public function _getCurrentUserCanLeave($queryId)
         if (!count(array_intersect([Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN, ], $userRoles))) {
             return false;
         }
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $participantIds = $queryDao->getParticipantIds($queryId);
+        $participantIds = QueryParticipant::withQueryId($queryId)
+            ->pluck('user_id')
+            ->all();
         if (count($participantIds) < 3) {
             return false;
         }
diff --git a/controllers/grid/queries/QueryNotesGridHandler.php b/controllers/grid/queries/QueryNotesGridHandler.php
index 357af98335d..18fc5b545f9 100644
--- a/controllers/grid/queries/QueryNotesGridHandler.php
+++ b/controllers/grid/queries/QueryNotesGridHandler.php
@@ -34,7 +34,7 @@
 use PKP\notification\Notification;
 use PKP\notification\NotificationSubscriptionSettingsDAO;
 use PKP\query\Query;
-use PKP\query\QueryDAO;
+use PKP\query\QueryParticipant;
 use PKP\security\authorization\QueryAccessPolicy;
 use PKP\security\Role;
 use PKP\submissionFile\SubmissionFile;
@@ -168,7 +168,7 @@ public function getRequestArgs()
         return [
             'submissionId' => $this->getSubmission()->getId(),
             'stageId' => $this->getStageId(),
-            'queryId' => $this->getQuery()->getId(),
+            'queryId' => $this->getQuery()->id,
         ];
     }
 
@@ -185,7 +185,7 @@ public function getRequestArgs()
      */
     public function loadData($request, $filter = null)
     {
-        return Note::withAssoc(PKPApplication::ASSOC_TYPE_QUERY, $this->getQuery()->getId())
+        return Note::withAssoc(PKPApplication::ASSOC_TYPE_QUERY, $this->getQuery()->id)
             ->withSort(Note::NOTE_ORDER_DATE_CREATED, DAO::SORT_DIRECTION_ASC)
             ->lazy()
             ->filter(function (Note $note) use ($request) {
@@ -222,7 +222,7 @@ public function insertNote($args, $request)
         if ($queryNoteForm->validate()) {
             $note = $queryNoteForm->execute();
             $this->insertedNoteNotify($note);
-            return DAO::getDataChangedEvent($this->getQuery()->getId());
+            return DAO::getDataChangedEvent($this->getQuery()->id);
         } else {
             return new JSONMessage(true, $queryNoteForm->fetch($request));
         }
@@ -258,7 +258,7 @@ public function deleteNote($args, $request)
         $query = $this->getQuery();
         $note = Note::find((int) $request->getUserVar('noteId'));
 
-        if (!$request->checkCSRF() || $note?->assocType != Application::ASSOC_TYPE_QUERY || $note?->assocId != $query->getId()) {
+        if (!$request->checkCSRF() || $note?->assocType != Application::ASSOC_TYPE_QUERY || $note?->assocId != $query->id) {
             // The note didn't exist or has the wrong assoc info.
             return new JSONMessage(false);
         }
@@ -278,13 +278,12 @@ public function deleteNote($args, $request)
     protected function insertedNoteNotify(Note $note): void
     {
         $notificationManager = new NotificationManager();
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $query = $queryDao->getById($note->assocId);
+        $query = Query::find($note->assocId);
         $sender = $note->user;
         $request = Application::get()->getRequest();
         $context = $request->getContext();
         $submission = $this->getSubmission();
-        $title = $query->getHeadNote()->title;
+        $title = Repo::note()->getHeadNote($query->id)->title;
 
         /** @var NotificationSubscriptionSettingsDAO $notificationSubscriptionSettingsDao */
         $notificationSubscriptionSettingsDao = DAORegistry::getDAO('NotificationSubscriptionSettingsDAO');
@@ -297,10 +296,12 @@ protected function insertedNoteNotify(Note $note): void
                 [$note->id]
             )->filterBySubmissionIds([$submission->getId()])
             ->getMany();
-
-        foreach ($queryDao->getParticipantIds($query->getId()) as $userId) {
+        $participantIds = QueryParticipant::withQueryId($query->id)
+            ->pluck('user_id')
+            ->all();
+        foreach ($participantIds as $userId) {
             // Delete any prior notifications of the same type (e.g. prior "new" comments)
-            Notification::withAssoc(PKPApplication::ASSOC_TYPE_QUERY, $query->getId())
+            Notification::withAssoc(PKPApplication::ASSOC_TYPE_QUERY, $query->id)
                 ->withUserId($userId)
                 ->withType(Notification::NOTIFICATION_TYPE_QUERY_ACTIVITY)
                 ->withContextId($context->getId())
@@ -323,7 +324,7 @@ protected function insertedNoteNotify(Note $note): void
                 Notification::NOTIFICATION_TYPE_QUERY_ACTIVITY,
                 $request->getContext()->getId(),
                 PKPApplication::ASSOC_TYPE_QUERY,
-                $query->getId(),
+                $query->id,
                 Notification::NOTIFICATION_LEVEL_TASK
             );
 
diff --git a/controllers/grid/queries/QueryNotesGridRow.php b/controllers/grid/queries/QueryNotesGridRow.php
index 705b230afdd..759ea80ad83 100644
--- a/controllers/grid/queries/QueryNotesGridRow.php
+++ b/controllers/grid/queries/QueryNotesGridRow.php
@@ -16,6 +16,7 @@
 
 namespace PKP\controllers\grid\queries;
 
+use APP\facades\Repo;
 use PKP\controllers\grid\GridRow;
 use PKP\linkAction\LinkAction;
 use PKP\linkAction\request\RemoteActionConfirmationModal;
@@ -63,7 +64,7 @@ public function initialize($request, $template = null)
 
         // Is this a new row or an existing row?
         $rowId = abs($this->getId());
-        $headNote = $this->getQuery()->getHeadNote();
+        $headNote = Repo::note()->getHeadNote($this->getQuery()->id);
         if ($rowId > 0 && $headNote?->id != $rowId) {
             // Only add row actions if this is an existing row
             $router = $request->getRouter();
diff --git a/controllers/grid/queries/QueryTitleGridColumn.php b/controllers/grid/queries/QueryTitleGridColumn.php
index ed5a9f97588..c38073f113a 100644
--- a/controllers/grid/queries/QueryTitleGridColumn.php
+++ b/controllers/grid/queries/QueryTitleGridColumn.php
@@ -3,8 +3,8 @@
 /**
  * @file controllers/grid/queries/QueryTitleGridColumn.php
  *
- * Copyright (c) 2014-2021 Simon Fraser University
- * Copyright (c) 2000-2021 John Willinsky
+ * Copyright (c) 2014-2024 Simon Fraser University
+ * Copyright (c) 2000-2024 John Willinsky
  * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
  *
  * @class QueryTitleGridColumn
@@ -16,6 +16,7 @@
 
 namespace PKP\controllers\grid\queries;
 
+use APP\facades\Repo;
 use PKP\controllers\grid\ColumnBasedGridCellProvider;
 use PKP\controllers\grid\GridColumn;
 use PKP\controllers\grid\GridHandler;
@@ -77,13 +78,13 @@ public function getCellActions($request, $row, $position = GridHandler::GRID_ACT
     {
         // Retrieve the submission file.
         $query = $row->getData();
-        $headNote = $query->getHeadNote();
+        $headNote = Repo::note()->getHeadNote($query->id);
 
         // Create the cell action to download a file.
         $router = $request->getRouter();
         $actionArgs = array_merge(
             $this->_actionArgs,
-            ['queryId' => $query->getId()]
+            ['queryId' => $query->id]
         );
 
         return array_merge(
diff --git a/controllers/grid/queries/form/QueryForm.php b/controllers/grid/queries/form/QueryForm.php
index 03a64eced8d..3f623f6db32 100644
--- a/controllers/grid/queries/form/QueryForm.php
+++ b/controllers/grid/queries/form/QueryForm.php
@@ -24,11 +24,15 @@
 use PKP\controllers\grid\queries\traits\StageMailable;
 use PKP\core\PKPApplication;
 use PKP\core\PKPRequest;
-use PKP\db\DAORegistry;
 use PKP\form\Form;
+use PKP\form\validation\FormValidator;
+use PKP\form\validation\FormValidatorCSRF;
+use PKP\form\validation\FormValidatorCustom;
+use PKP\form\validation\FormValidatorPost;
 use PKP\note\Note;
+use PKP\notification\Notification;
 use PKP\query\Query;
-use PKP\query\QueryDAO;
+use PKP\query\QueryParticipant;
 use PKP\security\Role;
 use PKP\stageAssignment\StageAssignment;
 use PKP\submission\reviewAssignment\ReviewAssignment;
@@ -67,44 +71,47 @@ public function __construct($request, $assocType, $assocId, $stageId, $queryId =
         parent::__construct('controllers/grid/queries/form/queryForm.tpl');
         $this->setStageId($stageId);
 
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
         if (!$queryId) {
             $this->_isNew = true;
 
             // Create a query
-            $query = $queryDao->newDataObject();
-            $query->setAssocType($assocType);
-            $query->setAssocId($assocId);
-            $query->setStageId($stageId);
-            $query->setSequence(REALLY_BIG_NUMBER);
-            $queryDao->insertObject($query);
-            $queryDao->resequence($assocType, $assocId);
+            $query = Query::create([
+                'assocType' => $assocType,
+                'assocId' => $assocId,
+                'stageId' => $stageId,
+                'seq' => REALLY_BIG_NUMBER
+            ]);
+
+            Repo::query()->resequence($assocType, $assocId);
 
             // Add the current user as a participant by default.
-            $queryDao->insertParticipant($query->getId(), $request->getUser()->getId());
+            QueryParticipant::create([
+                'queryId' => $query->id,
+                'userId' => $request->getUser()->getId()
+            ]);
 
             Note::create([
                 'userId' =>  $request->getUser()->getId(),
                 'assocType' => Application::ASSOC_TYPE_QUERY,
-                'assocId' => $query->getId(),
+                'assocId' => $query->id,
             ]);
         } else {
-            $query = $queryDao->getById($queryId, $assocType, $assocId);
+            $query = Query::find($queryId);
             assert(isset($query));
             // New queries will not have a head note.
-            $this->_isNew = !$query->getHeadNote();
+            $this->_isNew = !Repo::note()->getHeadNote($query->id);
         }
 
         $this->setQuery($query);
 
         // Validation checks for this form
-        $this->addCheck(new \PKP\form\validation\FormValidatorCustom($this, 'users', 'required', 'stageParticipants.notify.warning', function ($users) {
+        $this->addCheck(new FormValidatorCustom($this, 'users', 'required', 'stageParticipants.notify.warning', function ($users) {
             return count($users) > 1;
         }));
-        $this->addCheck(new \PKP\form\validation\FormValidator($this, 'subject', 'required', 'submission.queries.subjectRequired'));
-        $this->addCheck(new \PKP\form\validation\FormValidator($this, 'comment', 'required', 'submission.queries.messageRequired'));
-        $this->addCheck(new \PKP\form\validation\FormValidatorPost($this));
-        $this->addCheck(new \PKP\form\validation\FormValidatorCSRF($this));
+        $this->addCheck(new FormValidator($this, 'subject', 'required', 'submission.queries.subjectRequired'));
+        $this->addCheck(new FormValidator($this, 'comment', 'required', 'submission.queries.messageRequired'));
+        $this->addCheck(new FormValidatorPost($this));
+        $this->addCheck(new FormValidatorCSRF($this));
     }
 
     //
@@ -208,14 +215,15 @@ public function setAssocId($assocId)
      */
     public function initData()
     {
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
         if ($query = $this->getQuery()) {
-            $headNote = $query->getHeadNote();
+            $headNote = Repo::note()->getHeadNote($query->id);
             $this->_data = [
-                'queryId' => $query->getId(),
+                'queryId' => $query->id,
                 'subject' => $headNote?->title,
                 'comment' => $headNote?->contents,
-                'userIds' => $queryDao->getParticipantIds($query->getId()),
+                'userIds' => QueryParticipant::withQueryId($query->id)
+                    ->pluck('user_id')
+                    ->all(),
                 'template' => null,
             ];
         } else {
@@ -237,7 +245,7 @@ public function initData()
     public function fetch($request, $template = null, $display = false, $actionArgs = [])
     {
         $query = $this->getQuery();
-        $headNote = $query->getHeadNote();
+        $headNote = Repo::note()->getHeadNote($query->id);
         $user = $request->getUser();
         $context = $request->getContext();
 
@@ -248,16 +256,16 @@ public function fetch($request, $template = null, $display = false, $actionArgs
             'actionArgs' => $actionArgs,
             'csrfToken' => $request->getSession()->token(),
             'stageId' => $this->getStageId(),
-            'assocId' => $query->getAssocId(),
-            'assocType' => $query->getAssocType(),
+            'assocId' => $query->assocId,
+            'assocType' => $query->assocType,
         ]);
 
         // Queries only support Application::ASSOC_TYPE_SUBMISSION so far
-        if ($query->getAssocType() !== PKPApplication::ASSOC_TYPE_SUBMISSION) {
+        if ($query->assocType !== PKPApplication::ASSOC_TYPE_SUBMISSION) {
             return parent::fetch($request, $template, $display);
         }
 
-        $submission = Repo::submission()->get($query->getAssocId());
+        $submission = Repo::submission()->get($query->assocId);
 
         // Add the templates that can be used for this discussion
         $templateKeySubjectPairs = [];
@@ -280,8 +288,8 @@ public function fetch($request, $template = null, $display = false, $actionArgs
         $templateMgr->assign('templates', $templateKeySubjectPairs);
 
         // Get currently selected participants in the query
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $assignedParticipants = $query->getId() ? $queryDao->getParticipantIds($query->getId()) : [];
+
+        $assignedParticipants = $query->id ? QueryParticipant::withQueryId($query->id)->pluck('user_id')->all() : [];
 
         // Always include current user, even if not with a stage assignment
         $includeUsers[] = $user->getId();
@@ -293,8 +301,8 @@ public function fetch($request, $template = null, $display = false, $actionArgs
         $assignedRoles = (function () use ($query, $user) {
             $assignedRoles = [];
             // Replaces StageAssignmentDAO::getBySubmissionAndStageId
-            $usersAssignments = StageAssignment::withSubmissionIds([$query->getAssocId()])
-                ->withStageIds([$query->getStageId()])
+            $usersAssignments = StageAssignment::withSubmissionIds([$query->assocId])
+                ->withStageIds([$query->stageId])
                 ->withUserId($user->getId())
                 ->get();
 
@@ -305,7 +313,7 @@ public function fetch($request, $template = null, $display = false, $actionArgs
             return $assignedRoles;
         })();
 
-        if ($query->getStageId() == WORKFLOW_STAGE_ID_EXTERNAL_REVIEW || $query->getStageId() == WORKFLOW_STAGE_ID_INTERNAL_REVIEW) {
+        if ($query->stageId == WORKFLOW_STAGE_ID_EXTERNAL_REVIEW || $query->stageId == WORKFLOW_STAGE_ID_INTERNAL_REVIEW) {
             // Get all review assignments for current submission
             $reviewAssignments = Repo::reviewAssignment()->getCollector()->filterBySubmissionIds([$submission->getId()])->getMany();
 
@@ -321,7 +329,7 @@ public function fetch($request, $template = null, $display = false, $actionArgs
                 if ($reviewAssignment->getReviewerId() == $user->getId()) {
                     if ($reviewAssignment->getReviewMethod() != ReviewAssignment::SUBMISSION_REVIEW_METHOD_OPEN) {
                         // Replaces StageAssignmentDAO::getBySubmissionAndRoleId
-                        $excludeUsers = StageAssignment::withSubmissionIds([$query->getAssocId()])
+                        $excludeUsers = StageAssignment::withSubmissionIds([$query->assocId])
                             ->withRoleIds([Role::ROLE_ID_AUTHOR])
                             ->withUserId($user->getId())
                             ->get()
@@ -345,7 +353,7 @@ public function fetch($request, $template = null, $display = false, $actionArgs
             ->filterByContextIds([$context->getId()])
             ->limit(100)
             ->offset(0)
-            ->assignedTo($query->getAssocId(), $query->getStageId())
+            ->assignedTo($query->assocId, $query->stageId)
             ->excludeUserIds($excludeUsers)
             ->getMany();
 
@@ -358,8 +366,8 @@ public function fetch($request, $template = null, $display = false, $actionArgs
 
             $userRoles = [];
             // Replaces StageAssignmentDAO::getBySubmissionAndStageId
-            $userAssignments = StageAssignment::withSubmissionIds([$query->getAssocId()])
-                ->withStageIds([$query->getStageId()])
+            $userAssignments = StageAssignment::withSubmissionIds([$query->assocId])
+                ->withStageIds([$query->stageId])
                 ->withUserId($user->getId())
                 ->get();
 
@@ -428,12 +436,12 @@ public function validate($callHooks = true)
         // In other stages validate that participants are assigned to that stage.
         $query = $this->getQuery();
         // Queries only support Application::ASSOC_TYPE_SUBMISSION so far (see above)
-        if ($query->getAssocType() == Application::ASSOC_TYPE_SUBMISSION) {
+        if ($query->assocType == Application::ASSOC_TYPE_SUBMISSION) {
             $request = Application::get()->getRequest();
             $user = $request->getUser();
             $context = $request->getContext();
-            $submissionId = $query->getAssocId();
-            $stageId = $query->getStageId();
+            $submissionId = $query->assocId;
+            $stageId = $query->stageId;
 
             // get the selected participants
             $newParticipantIds = (array) $this->getData('users');
@@ -509,37 +517,43 @@ public function validate($callHooks = true)
      */
     public function execute(...$functionArgs)
     {
-        $request = Application::get()->getRequest();
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
         $query = $this->getQuery();
 
-        $headNote = $query->getHeadNote();
+        $headNote = Repo::note()->getHeadNote($query->id);
         $headNote->title = $this->getData('subject');
         $headNote->contents = $this->getData('comment');
-
         $headNote->save();
 
-        $queryDao->updateObject($query);
+        $query->update();
 
         // Update participants
-        $oldParticipantIds = $queryDao->getParticipantIds($query->getId());
+        $oldParticipantIds = QueryParticipant::withQueryId($query->id)
+            ->pluck('user_id')
+            ->all();
+
         $newParticipantIds = $this->getData('users');
-        $queryDao->removeAllParticipants($query->getId());
+        QueryParticipant::withQueryId($query->id)
+            ->delete();
+        $addParticipants = [];
         foreach ($newParticipantIds as $userId) {
-            $queryDao->insertParticipant($query->getId(), $userId);
+            $addParticipants[] = ([
+                'query_id' => $query->id,
+                'user_id' => $userId
+            ]);
         }
+        QueryParticipant::insert($addParticipants);
 
         $removed = array_diff($oldParticipantIds, $newParticipantIds);
         foreach ($removed as $userId) {
             // Delete this users' notifications relating to this query
-            Notification::withAssoc(Application::ASSOC_TYPE_QUERY, $query->getId())
+            Notification::withAssoc(Application::ASSOC_TYPE_QUERY, $query->id)
                 ->withUserId($userId)
                 ->delete();
         }
 
         // Stamp the submission status modification date.
-        if ($query->getAssocType() == Application::ASSOC_TYPE_SUBMISSION) {
-            $submission = Repo::submission()->get($query->getAssocId());
+        if ($query->assocType == Application::ASSOC_TYPE_SUBMISSION) {
+            $submission = Repo::submission()->get($query->assocId);
             $submission->stampLastActivity();
             Repo::submission()->dao->update($submission);
         }
diff --git a/controllers/grid/queries/form/QueryNoteForm.php b/controllers/grid/queries/form/QueryNoteForm.php
index d84ee642311..378535dd344 100644
--- a/controllers/grid/queries/form/QueryNoteForm.php
+++ b/controllers/grid/queries/form/QueryNoteForm.php
@@ -17,13 +17,15 @@
 namespace PKP\controllers\grid\queries\form;
 
 use APP\core\Application;
+use APP\facades\Repo;
 use APP\template\TemplateManager;
-use PKP\core\Core;
-use PKP\db\DAORegistry;
 use PKP\form\Form;
+use PKP\form\validation\FormValidator;
+use PKP\form\validation\FormValidatorCSRF;
+use PKP\form\validation\FormValidatorPost;
 use PKP\note\Note;
 use PKP\query\Query;
-use PKP\query\QueryDAO;
+use PKP\query\QueryParticipant;
 use PKP\user\User;
 
 class QueryNoteForm extends Form
@@ -58,7 +60,7 @@ public function __construct($actionArgs, $query, $user, $noteId = null)
             // Create a new (placeholder) note.
             $note = new Note;
             $note->assocType = Application::ASSOC_TYPE_QUERY;
-            $note->assocId = $query->getId();
+            $note->assocId = $query->id;
             $note->userId = $user->getId();
             $note->save();
             $this->_noteId = $note->id;
@@ -69,9 +71,9 @@ public function __construct($actionArgs, $query, $user, $noteId = null)
         }
 
         // Validation checks for this form
-        $this->addCheck(new \PKP\form\validation\FormValidator($this, 'comment', 'required', 'submission.queries.messageRequired'));
-        $this->addCheck(new \PKP\form\validation\FormValidatorPost($this));
-        $this->addCheck(new \PKP\form\validation\FormValidatorCSRF($this));
+        $this->addCheck(new FormValidator($this, 'comment', 'required', 'submission.queries.messageRequired'));
+        $this->addCheck(new FormValidatorPost($this));
+        $this->addCheck(new FormValidatorCSRF($this));
     }
 
     //
@@ -140,23 +142,26 @@ public function execute(...$functionArgs)
         $note->contents = $this->getData('comment');
         $note->save();
 
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-
         // Check whether the query needs re-opening
         $query = $this->getQuery();
-        if ($query->getIsClosed()) {
-            $headNote = $query->getHeadNote();
+        if ($query->closed) {
+            $headNote = Repo::note()->getHeadNote($query->id);
             if ($user->getId() != $headNote->userId) {
                 // Re-open the query.
-                $query->setIsClosed(false);
-                $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-                $queryDao->updateObject($query);
+                $query->closed = false;
+                $query->save();
             }
         }
 
         // Always include current user to query participants
-        if (!in_array($user->getId(), $queryDao->getParticipantIds($query->getId()))) {
-            $queryDao->insertParticipant($query->getId(), $user->getId());
+        $participantIds = QueryParticipant::withQueryId($query->id)
+            ->pluck('user_id')
+            ->all();
+        if (!in_array($user->getId(), $participantIds)) {
+            QueryParticipant::create([
+                'queryId' => $query->id,
+                'userId' => $user->getId()
+            ]);
         }
 
         parent::execute(...$functionArgs);
diff --git a/controllers/grid/users/stageParticipant/form/PKPStageParticipantNotifyForm.php b/controllers/grid/users/stageParticipant/form/PKPStageParticipantNotifyForm.php
index 8309318084c..55ffecfaaa6 100644
--- a/controllers/grid/users/stageParticipant/form/PKPStageParticipantNotifyForm.php
+++ b/controllers/grid/users/stageParticipant/form/PKPStageParticipantNotifyForm.php
@@ -27,13 +27,16 @@
 use PKP\core\Core;
 use PKP\core\PKPApplication;
 use PKP\core\PKPRequest;
-use PKP\db\DAORegistry;
 use PKP\form\Form;
+use PKP\form\validation\FormValidator;
+use PKP\form\validation\FormValidatorCSRF;
+use PKP\form\validation\FormValidatorPost;
 use PKP\log\event\EventLogEntry;
 use PKP\log\SubmissionEmailLogEventType;
 use PKP\note\Note;
 use PKP\notification\Notification;
-use PKP\query\QueryDAO;
+use PKP\query\Query;
+use PKP\query\QueryParticipant;
 use PKP\security\Role;
 use PKP\security\Validation;
 use Symfony\Component\Mailer\Exception\TransportException;
@@ -77,11 +80,11 @@ public function __construct($itemId, $itemType, $stageId, $template = null)
         // Some other forms (e.g. the Add Participant form) subclass this form and
         // may not enforce the sending of an email.
         if ($this->isMessageRequired()) {
-            $this->addCheck(new \PKP\form\validation\FormValidator($this, 'message', 'required', 'stageParticipants.notify.warning'));
+            $this->addCheck(new FormValidator($this, 'message', 'required', 'stageParticipants.notify.warning'));
         }
-        $this->addCheck(new \PKP\form\validation\FormValidator($this, 'userId', 'required', 'stageParticipants.notify.warning'));
-        $this->addCheck(new \PKP\form\validation\FormValidatorPost($this));
-        $this->addCheck(new \PKP\form\validation\FormValidatorCSRF($this));
+        $this->addCheck(new FormValidator($this, 'userId', 'required', 'stageParticipants.notify.warning'));
+        $this->addCheck(new FormValidatorPost($this));
+        $this->addCheck(new FormValidatorCSRF($this));
     }
 
     /**
@@ -175,19 +178,25 @@ public function sendMessage(int $userId, Submission $submission, Request $reques
         }
 
         // Create a query
-        $queryDao = DAORegistry::getDAO('QueryDAO'); /** @var QueryDAO $queryDao */
-        $query = $queryDao->newDataObject();
-        $query->setAssocType(PKPApplication::ASSOC_TYPE_SUBMISSION);
-        $query->setAssocId($submission->getId());
-        $query->setStageId($this->_stageId);
-        $query->setSequence(REALLY_BIG_NUMBER);
-        $queryDao->insertObject($query);
-        $queryDao->resequence(PKPApplication::ASSOC_TYPE_SUBMISSION, $submission->getId());
+        $query = Query::create([
+            'assocType' => PKPApplication::ASSOC_TYPE_SUBMISSION,
+            'assocId' => $submission->getId(),
+            'stageId' => $this->_stageId,
+            'seq' => REALLY_BIG_NUMBER
+        ]);
+
+        Repo::query()->resequence(PKPApplication::ASSOC_TYPE_SUBMISSION, $submission->getId());
 
         // Add the current user and message recipient as participants.
-        $queryDao->insertParticipant($query->getId(), $user->getId());
+        QueryParticipant::create([
+            'queryId' => $query->id,
+            'userId' => $user->getId()
+        ]);
         if ($user->getId() != $request->getUser()->getId()) {
-            $queryDao->insertParticipant($query->getId(), $request->getUser()->getId());
+            QueryParticipant::create([
+                'queryId' => $query->id,
+                'userId' => $request->getUser()->getId()
+            ]);
         }
 
         // Populate mailable with data before compiling headNote
@@ -205,7 +214,7 @@ public function sendMessage(int $userId, Submission $submission, Request $reques
         $headNote = Note::create([
             'userId' =>  $request->getUser()->getId(),
             'assocType' => PKPApplication::ASSOC_TYPE_QUERY,
-            'assocId' => $query->getId(),
+            'assocId' => $query->id,
             'title' => Mail::compileParams(
                 $template->getLocalizedData('subject'),
                 $mailable->getData()
@@ -224,7 +233,7 @@ public function sendMessage(int $userId, Submission $submission, Request $reques
             Notification::NOTIFICATION_TYPE_NEW_QUERY,
             $request->getContext()->getId(),
             PKPApplication::ASSOC_TYPE_QUERY,
-            $query->getId(),
+            $query->id,
             Notification::NOTIFICATION_LEVEL_TASK
         );
 
diff --git a/templates/controllers/grid/queries/readQuery.tpl b/templates/controllers/grid/queries/readQuery.tpl
index 5c6de7f8682..80620772af6 100644
--- a/templates/controllers/grid/queries/readQuery.tpl
+++ b/templates/controllers/grid/queries/readQuery.tpl
@@ -13,8 +13,8 @@
 		$('#readQueryContainer').pkpHandler(
 			'$.pkp.controllers.grid.queries.ReadQueryHandler',
 			{ldelim}
-				fetchNoteFormUrl: {url|json_encode router=PKP\core\PKPApplication::ROUTE_COMPONENT component=$queryNotesGridHandlerName op="addNote" params=$requestArgs queryId=$query->getId() escape=false},
-				fetchParticipantsListUrl: {url|json_encode router=PKP\core\PKPApplication::ROUTE_COMPONENT component="grid.queries.QueriesGridHandler" op="participants" params=$requestArgs queryId=$query->getId() escape=false}
+				fetchNoteFormUrl: {url|json_encode router=PKP\core\PKPApplication::ROUTE_COMPONENT component=$queryNotesGridHandlerName op="addNote" params=$requestArgs queryId=$query->id escape=false},
+				fetchParticipantsListUrl: {url|json_encode router=PKP\core\PKPApplication::ROUTE_COMPONENT component="grid.queries.QueriesGridHandler" op="participants" params=$requestArgs queryId=$query->id escape=false}
 			{rdelim}
 		);
 	{rdelim});
@@ -29,7 +29,7 @@
     </h4>
     <ul id="participantsListPlaceholder" class="participants"></ul>
 
-	{capture assign=queryNotesGridUrl}{url router=PKP\core\PKPApplication::ROUTE_COMPONENT component=$queryNotesGridHandlerName op="fetchGrid" params=$requestArgs queryId=$query->getId() escape=false}{/capture}
+	{capture assign=queryNotesGridUrl}{url router=PKP\core\PKPApplication::ROUTE_COMPONENT component=$queryNotesGridHandlerName op="fetchGrid" params=$requestArgs queryId=$query->id escape=false}{/capture}
 	{load_url_in_div id="queryNotesGrid" url=$queryNotesGridUrl}
 
 	<div class="queryEditButtons">