pkp · Hafsa-Naeem · Mar 9, 2026
diff --git a/classes/editorialTask/EditorialTask.php b/classes/editorialTask/EditorialTask.php
@@ -325,6 +325,7 @@ protected function fillHeadnote(array $attributes): array
                 'userId' => $attributes['createdBy'] ?? $this->createdBy,
                 'contents' => $attributes[self::ATTRIBUTE_HEADNOTE],
                 'isHeadnote' => true,
+                'messageId' => Note::generateMessageId(),
             ]);
 
             unset($attributes[self::ATTRIBUTE_HEADNOTE]);

diff --git a/classes/editorialTask/Repository.php b/classes/editorialTask/Repository.php
@@ -32,6 +32,11 @@
 use PKP\security\Role;
 use PKP\stageAssignment\StageAssignment;
 use PKP\user\User;
+use PKP\mail\mailables\DiscussionSubmission;
+use PKP\mail\mailables\DiscussionReview;
+use PKP\mail\mailables\DiscussionCopyediting;
+use PKP\mail\mailables\DiscussionProduction;
+
 
 class Repository
 {
@@ -46,7 +51,7 @@ public function countOpenPerStage(int $submissionId, ?array $participantIds = nu
     {
         $counts = EditorialTask::withAssoc(Application::ASSOC_TYPE_SUBMISSION, $submissionId)
             ->when($participantIds !== null, function ($q) use ($participantIds) {
-                $q->withUserIds($participantIds);
+                $q->withParticipantIds($participantIds);
             })
             ->withClosed(false)
             ->selectRaw('stage_id, COUNT(stage_id) as count')
@@ -96,15 +101,21 @@ public function addQuery(int $submissionId, int $stageId, string $title, string
             'seq' => $maxSeq + 1,
             'createdBy' => $fromUser->getId(),
             'type' => EditorialTaskType::DISCUSSION->value,
-            EditorialTask::ATTRIBUTE_PARTICIPANTS => array_map(fn (int $participantId) => ['userId' => $participantId], array_unique($participantUserIds)),
+            EditorialTask::ATTRIBUTE_PARTICIPANTS => array_map(
+                fn (int $participantId) => ['userId' => $participantId],
+                array_unique($participantUserIds)
+            ),
             'title' => $title,
         ]);
 
-        Note::create([
+        // Head note for this discussion, with a capturable messageId
+        $headNote = Note::create([
             'assocType' => Application::ASSOC_TYPE_QUERY,
             'assocId' => $task->id,
             'contents' => $content,
             'userId' => $fromUser->getId(),
+            'isHeadnote' => true,
+            'messageId' => Note::generateMessageId(),
         ]);
 
         // Add task for assigned participants
@@ -113,8 +124,24 @@ public function addQuery(int $submissionId, int $stageId, string $title, string
         /** @var NotificationSubscriptionSettingsDAO $notificationSubscriptionSettingsDao */
         $notificationSubscriptionSettingsDao = DAORegistry::getDAO('NotificationSubscriptionSettingsDAO');
 
+        // need submission + context + stage mailables to send capturable email
+        $submission = Repo::submission()->get($submissionId);
+        $application = Application::get();
+        $request = $application->getRequest();
+        $context = $request?->getContext();
+
+        $mailableMap = [
+            WORKFLOW_STAGE_ID_SUBMISSION => DiscussionSubmission::class,
+            WORKFLOW_STAGE_ID_INTERNAL_REVIEW => DiscussionReview::class,
+            WORKFLOW_STAGE_ID_EXTERNAL_REVIEW => DiscussionReview::class,
+            WORKFLOW_STAGE_ID_EDITING => DiscussionCopyediting::class,
+            WORKFLOW_STAGE_ID_PRODUCTION => DiscussionProduction::class,
+        ];
+
+        $mailableClass = $mailableMap[$stageId] ?? null;
+
         foreach ($task->participants()->get() as $participant) {
-            $notificationMgr->createNotification(
+            $notification = $notificationMgr->createNotification(
                 $participant->userId,
                 Notification::NOTIFICATION_TYPE_NEW_QUERY,
                 $contextId,
@@ -123,7 +150,8 @@ public function addQuery(int $submissionId, int $stageId, string $title, string
                 Notification::NOTIFICATION_LEVEL_TASK
             );
 
-            if (!$sendEmail) {
+            if (
+                !$sendEmail|| !$notification || !$mailableClass || !$submission || !$context) {
                 continue;
             }
 
@@ -138,11 +166,20 @@ public function addQuery(int $submissionId, int $stageId, string $title, string
             }
 
             $recipient = $participant->user;
-            $mailable = new Mailable();
-            $mailable->to($recipient->getEmail(), $recipient->getFullName());
-            $mailable->from($fromUser->getEmail(), $fromUser->getFullName());
-            $mailable->subject($title);
-            $mailable->body($content);
+            if (!$recipient) {
+                continue;
+            }
+
+            /** @var \PKP\mail\Mailable $mailable */
+            $mailable = new $mailableClass($context, $submission);
+
+            $mailable
+                ->sender($fromUser)
+                ->recipients([$recipient])
+                ->subject($title)
+                ->body($content)
+                ->allowUnsubscribe($notification)
+                ->allowCapturableReply($headNote->messageId);
 
             Mail::send($mailable);
         }
@@ -250,6 +287,152 @@ public function deleteBySubmissionId(int $submissionId): void
         }
     }
 
+    public function notifyParticipantsOnNote(Note $note): void
+    {
+        // Only discussion notes
+        if ($note->assocType !== PKPApplication::ASSOC_TYPE_QUERY) {
+            return;
+        }
+
+        // skip headnote initial email handled when query is created
+        if ($note->isHeadnote ?? false) {
+            return;
+        }
+
+        $task = EditorialTask::find($note->assocId);
+        if (!$task) {
+            return;
+        }
+
+        $submission = Repo::submission()->get($task->assocId);
+        if (!$submission) {
+            return;
+        }
+
+        $application = Application::get();
+        $request = $application->getRequest();
+        $context = $request->getContext();
+        if (!$context) {
+            return;
+        }
+
+        $sender = Repo::user()->get($note->userId ?? null);
+        if (!$sender) {
+            return;
+        }
+
+        $headNote = Repo::note()->getHeadNote($task->id);
+        $threadAnchorMessageId = $headNote?->messageId;
+        $title = $headNote?->title ?: $task->title;
+        $subject = $title
+            ? __('common.re') . ' ' . $title
+            : __('common.re');
+
+
+        $participantIds = $task->participants()
+            ->pluck('user_id')
+            ->all();
+
+        if (empty($participantIds)) {
+            return;
+        }
+
+        /** @var NotificationSubscriptionSettingsDAO $notificationSubscriptionSettingsDao */
+        $notificationSubscriptionSettingsDao = DAORegistry::getDAO('NotificationSubscriptionSettingsDAO');
+
+        $notificationManager = new NotificationManager();
+
+        // attachments for this note (if any)
+        $submissionFiles = Repo::submissionFile()
+            ->getCollector()
+            ->filterByAssoc(PKPApplication::ASSOC_TYPE_NOTE, [$note->id])
+            ->filterBySubmissionIds([$submission->getId()])
+            ->getMany();
+
+        // Stage -> mailable map (same as StageMailable)
+        $mailableMap = [
+            WORKFLOW_STAGE_ID_SUBMISSION => DiscussionSubmission::class,
+            WORKFLOW_STAGE_ID_INTERNAL_REVIEW => DiscussionReview::class,
+            WORKFLOW_STAGE_ID_EXTERNAL_REVIEW => DiscussionReview::class,
+            WORKFLOW_STAGE_ID_EDITING => DiscussionCopyediting::class,
+            WORKFLOW_STAGE_ID_PRODUCTION => DiscussionProduction::class,
+        ];
+
+        if (!isset($mailableMap[$task->stageId])) {
+            return;
+        }
+
+        $mailableClass = $mailableMap[$task->stageId];
+
+        foreach ($participantIds as $userId) {
+            if ($userId === $sender->getId()) {
+                continue;
+            }
+
+            // clear previous "query activity" notifications for this user/query
+            Notification::withAssoc(PKPApplication::ASSOC_TYPE_QUERY, $task->id)
+                ->withUserId($userId)
+                ->withType(Notification::NOTIFICATION_TYPE_QUERY_ACTIVITY)
+                ->withContextId((int) $context->getId())
+                ->delete();
+
+            $recipient = Repo::user()->get($userId);
+            if (!$recipient) {
+                continue;
+            }
+
+            // create notification
+            $notification = $notificationManager->createNotification(
+                $userId,
+                Notification::NOTIFICATION_TYPE_QUERY_ACTIVITY,
+                (int) $context->getId(),
+                PKPApplication::ASSOC_TYPE_QUERY,
+                $task->id,
+                Notification::NOTIFICATION_LEVEL_TASK
+            );
+
+            if (!$notification) {
+                continue;
+            }
+
+            // respect email notification settings
+            $blocked = $notificationSubscriptionSettingsDao->getNotificationSubscriptionSettings(
+                NotificationSubscriptionSettingsDAO::BLOCKED_EMAIL_NOTIFICATION_KEY,
+                $userId,
+                (int) $context->getId()
+            );
+
+            if (in_array(Notification::NOTIFICATION_TYPE_QUERY_ACTIVITY, $blocked)) {
+                continue;
+            }
+
+            /** @var \PKP\mail\Mailable $mailable */
+            $mailable = new $mailableClass($context, $submission);
+
+            $mailable
+                ->sender($sender)
+                ->recipients([$recipient])
+                ->subject($subject)
+                ->body($note->contents)
+                ->allowUnsubscribe($notification)
+                ->allowCapturableReply(
+                    $note->messageId,
+                    $threadAnchorMessageId && $threadAnchorMessageId !== $note->messageId ? $threadAnchorMessageId : null,
+                    $threadAnchorMessageId ? [$threadAnchorMessageId] : []
+                );
+
+            $submissionFiles->each(
+                fn ($item) => $mailable->attachSubmissionFile(
+                    $item->getId(),
+                    $item->getData('name')
+                )
+            );
+
+            Mail::send($mailable);
+        }
+    }
+
+
     public function removeParticipantFromSubmissionTasks(int $submissionId, int $userId, int $contextId): void
     {
         $user = Repo::user()->get($userId);

diff --git a/classes/mail/traits/CapturableReply.php b/classes/mail/traits/CapturableReply.php
@@ -0,0 +1,64 @@
+<?php
+
+/**
+ * @file classes/mail/traits/CapturableReply.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 CapturableReply
+ *
+ * @ingroup mail_traits
+ *
+ * @brief Mailable trait to add support for capturable replies
+ */
+
+namespace PKP\mail\traits;
+
+use Illuminate\Mail\Mailables\Headers;
+use PKP\config\Config;
+
+trait CapturableReply
+{
+    protected ?string $messageId = null;
+    protected ?string $inReplyTo = null;
+    protected array $references = [];
+
+    /**
+     * Adds headers that can be used to determine what a reply is in response to
+     */
+    public function headers(): Headers
+    {
+        $textHeaders = [];
+
+        if ($this->inReplyTo) {
+            $textHeaders['In-Reply-To'] = $this->inReplyTo;
+        }
+
+        return new Headers(
+            messageId: $this->messageId ?: null,
+            references: $this->references,
+            text: $textHeaders,
+        );
+    }
+
+    public function setupCapturableReply()
+    {
+        if ($replyTo = Config::getVar('email', 'reply_to_address')) {
+            $this->replyTo($replyTo);
+        }
+    }
+
+    public function allowCapturableReply(
+        ?string $messageId,
+        ?string $inReplyTo = null,
+        array $references = []
+    ): static {
+        $this->messageId = $messageId;
+        $this->inReplyTo = $inReplyTo;
+        $this->references = $references;
+
+        return $this;
+    }
+}
diff --git a/classes/mail/traits/Discussion.php b/classes/mail/traits/Discussion.php
@@ -16,17 +16,40 @@
 
 namespace PKP\mail\traits;
 
+use Illuminate\Mail\Mailables\Headers;
 use PKP\mail\variables\SubmissionEmailVariable;
 
 trait Discussion
 {
-    use Unsubscribe {
-        getRequiredVariables as getTraitRequiredVariables;
+    use Unsubscribe, CapturableReply {
+        Unsubscribe::getRequiredVariables as getTraitRequiredVariables;
+        Unsubscribe::headers as unsubscribeHeaders;
+        CapturableReply::headers as capturableReplyHeaders;
+    }
+
+    /**
+     * Merge the headers from the competing traits together.
+     */
+    public function headers(): Headers
+    {
+        $unsubscribeHeaders = $this->unsubscribeHeaders();
+        $capturableReplyHeaders = $this->capturableReplyHeaders();
+
+        if ($unsubscribeHeaders->messageId !== null) {
+            throw new \Exception('Unable to merge message IDs!');
+        }
+
+        return new Headers(
+            $capturableReplyHeaders->messageId,
+            array_merge($unsubscribeHeaders->references, $capturableReplyHeaders->references),
+            array_merge($unsubscribeHeaders->text, $capturableReplyHeaders->text)
+        );
     }
 
     protected function addFooter(string $locale): self
     {
         $this->setupUnsubscribeFooter($locale, $this->context);
+        $this->setupCapturableReply();
         return $this;
     }
 

diff --git a/classes/migration/install/NotesMigration.php b/classes/migration/install/NotesMigration.php
@@ -36,10 +36,12 @@ public function up(): void
 
             $table->datetime('date_created');
             $table->datetime('date_modified')->nullable();
+            $table->string('message_id', 255)->nullable();
             $table->text('contents')->nullable();
             $table->boolean('is_headnote')->default(false);
 
             $table->index(['assoc_type', 'assoc_id'], 'notes_assoc');
+            $table->index(['message_id'], 'notes_message_id');
         });
     }