From 297cdc5a1f100e58bb0fd91ae5af3ae37e069cf9 Mon Sep 17 00:00:00 2001
From: Jonas Raoni Soares da Silva <github@raoni.org>
Date: Sat, 23 Dec 2023 18:58:45 +0300
Subject: [PATCH 1/2] pkp/pkp-lib#9535 Skipped submission files that have an
 invalid file stage at the Native XML plugin

---
 locale/en/manager.po                                       | 3 +++
 .../native/filter/SubmissionFileNativeXmlFilter.php        | 7 +++++++
 2 files changed, 10 insertions(+)

diff --git a/locale/en/manager.po b/locale/en/manager.po
index 820c8b921a2..45e61dae8fd 100644
--- a/locale/en/manager.po
+++ b/locale/en/manager.po
@@ -2263,6 +2263,9 @@ msgstr ""
 msgid "plugins.importexport.native.error.submissionFileWithoutRevision"
 msgstr "The submission file {$id} was skipped because it does not have a valid revision."
 
+msgid "plugins.importexport.native.error.submissionFileInvalidFileStage"
+msgstr "The submission file {$id} was skipped because it does not have a valid file stage."
+
 msgid "plugins.importexport.native.error.submissionFileRevisionMissing"
 msgstr "The revision {$revision} of the submission file {$id} was skipped because the file was not found at the path \"{$path}\"."
 
diff --git a/plugins/importexport/native/filter/SubmissionFileNativeXmlFilter.php b/plugins/importexport/native/filter/SubmissionFileNativeXmlFilter.php
index b4c22b9f3fb..99b32b6cd0c 100644
--- a/plugins/importexport/native/filter/SubmissionFileNativeXmlFilter.php
+++ b/plugins/importexport/native/filter/SubmissionFileNativeXmlFilter.php
@@ -81,6 +81,13 @@ public function createSubmissionFileNode(DOMDocument $doc, SubmissionFile $submi
         $deployment = $this->getDeployment();
         $context = $deployment->getContext();
         $stageToName = array_flip($deployment->getStageNameStageIdMapping());
+
+        // Quit if the submission file has an invalid file stage
+        if (!isset($stageToName[$submissionFile->getFileStage()])) {
+            $deployment->addWarning(PKPApplication::ASSOC_TYPE_SUBMISSION_FILE, $submissionFile->getId(), __('plugins.importexport.native.error.submissionFileInvalidFileStage', ['id' => $submissionFile->getId()]));
+            return null;
+        }
+
         $genreDao = DAORegistry::getDAO('GenreDAO'); /** @var GenreDAO $genreDao */
         $genre = $genreDao->getById($submissionFile->getData('genreId'));
         $uploaderUser = Repo::user()->get($submissionFile->getData('uploaderUserId'), true);

From 61b0e3510068b530e37142d79e75dd53d1b56b2f Mon Sep 17 00:00:00 2001
From: Jonas Raoni Soares da Silva <github@raoni.org>
Date: Sat, 30 Dec 2023 19:52:15 +0300
Subject: [PATCH 2/2] pkp/pkp-lib#9535 Added migration to move zeroed file
 stages to the submission stage

---
 .../v3_4_0/I9535_FixEmptyFileStage.php        | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 classes/migration/upgrade/v3_4_0/I9535_FixEmptyFileStage.php

diff --git a/classes/migration/upgrade/v3_4_0/I9535_FixEmptyFileStage.php b/classes/migration/upgrade/v3_4_0/I9535_FixEmptyFileStage.php
new file mode 100644
index 00000000000..5289caf5b11
--- /dev/null
+++ b/classes/migration/upgrade/v3_4_0/I9535_FixEmptyFileStage.php
@@ -0,0 +1,37 @@
+<?php
+
+/**
+ * @file classes/migration/upgrade/v3_4_0/I9535_FixEmptyFileStage.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 I9535_FixEmptyFileStage.php
+ *
+ * @brief Redirect empty file stages to the SUBMISSION_FILE_SUBMISSION.
+ *
+ */
+
+namespace PKP\migration\upgrade\v3_4_0;
+
+use Illuminate\Support\Facades\DB;
+use PKP\install\DowngradeNotSupportedException;
+use PKP\migration\Migration;
+
+class I9535_FixEmptyFileStage extends Migration
+{
+    public function up(): void
+    {
+        DB::table('submission_files')
+            // empty file_stage
+            ->where('file_stage', 0)
+            // To \PKP\submissionFile\SubmissionFile::SUBMISSION_FILE_SUBMISSION
+            ->update(['file_stage' => 2]);
+    }
+
+    public function down(): void
+    {
+        throw new DowngradeNotSupportedException();
+    }
+}