From c15f8a1312143908e5651fa50daca49a8e06b79e Mon Sep 17 00:00:00 2001
From: Bozana Bokan <bozana.bokan@posteo.net>
Date: Mon, 16 Dec 2024 20:26:12 +0100
Subject: [PATCH 1/2] fix deprecated submission functions

---
 SwordHandler.php                |  2 +-
 SwordImportExportPlugin.php     |  2 +-
 SwordPlugin.php                 |  4 ++--
 classes/PKPSwordDeposit.php     | 17 ++++++++---------
 templates/authorDepositForm.tpl |  4 ++--
 5 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/SwordHandler.php b/SwordHandler.php
index 9a7e749..0942652 100644
--- a/SwordHandler.php
+++ b/SwordHandler.php
@@ -115,7 +115,7 @@ public function index($args, $request) {
 		$submission = $submissionDao->getById($submissionId);
 
 		if (!$submission || !$user || !$context ||
-			($submission->getContextId() != $context->getId())) {
+			($submission->getData('contextId') != $context->getId())) {
 				$request->redirect(null, 'index');
 		}
 
diff --git a/SwordImportExportPlugin.php b/SwordImportExportPlugin.php
index 0df6d0f..4672fce 100644
--- a/SwordImportExportPlugin.php
+++ b/SwordImportExportPlugin.php
@@ -219,7 +219,7 @@ public function display($args, $request) {
 						}
 						catch (\Exception $e) {
 							$errors[] = [
-								'title' => $submission->getLocalizedTitle(),
+								'title' => $submission->getCurrentPublication()->getLocalizedTitle(),
 								'message' => $e->getMessage(),
 							];
 						}
diff --git a/SwordPlugin.php b/SwordPlugin.php
index 32e0dc1..801d1ff 100644
--- a/SwordPlugin.php
+++ b/SwordPlugin.php
@@ -167,7 +167,7 @@ function performAutomaticDeposits(Submission $submission) {
 					NOTIFICATION_TYPE_SUCCESS,
 					[
 						'contents' => __('plugins.generic.sword.automaticDepositComplete', [
-							'itemTitle' => $submission->getLocalizedTitle(),
+							'itemTitle' => $submission->getCurrentPublication()->getLocalizedTitle(),
 							'repositoryName' => $depositPoint->getLocalizedName()
 						])
 					]
@@ -207,7 +207,7 @@ function performAutomaticDeposits(Submission $submission) {
 
 				$mail->assignParams([
 					'contextName' => htmlspecialchars($context->getLocalizedName()),
-					'submissionTitle' => htmlspecialchars($submission->getLocalizedTitle()),
+					'submissionTitle' => htmlspecialchars($submission->getCurrentPublication()->getLocalizedTitle()),
 					'swordDepositUrl' => $dispatcher->url(
 						$request, ROUTE_PAGE, null, 'sword', 'index', $submission->getId()
 					)
diff --git a/classes/PKPSwordDeposit.php b/classes/PKPSwordDeposit.php
index 236715c..be7fdb1 100644
--- a/classes/PKPSwordDeposit.php
+++ b/classes/PKPSwordDeposit.php
@@ -17,7 +17,6 @@
 
 use PKP\submissionFile\SubmissionFile;
 use PKP\file\FileManager;
-use PKP\db\DAORegistry;
 
 use APP\facades\Repo;
 use APP\core\Application;
@@ -29,10 +28,10 @@
 require_once dirname(__FILE__) . '/../libs/swordappv2/swordappentry.php';
 
 class PKPSwordDeposit {
-	/** @var SWORD deposit METS package */
+	/** @var PKPPackagerMetsSwap SWORD deposit METS package */
 	protected $_package = null;
 
-	/** @var Complete path and directory name to use for package creation files */
+	/** @var string Complete path and directory name to use for package creation files */
 	protected $_outPath = null;
 
 	/** @var Journal */
@@ -45,7 +44,7 @@ class PKPSwordDeposit {
 	protected $_issue = null;
 
 	/** @var Article */
-	protected $_article = null;
+	protected $_submission = null;
 
 	/**
 	 * Constructor.
@@ -72,7 +71,7 @@ public function __construct($submission) {
 		$application = Application::get();
 		$publication = $submission->getCurrentPublication();
 
-		$this->_context = $application->getContextDao()->getById($submission->getContextId());
+		$this->_context = $application->getContextDao()->getById($submission->getData('contextId'));
 
 		$this->_section = Repo::section()->get($publication->getData('sectionId'));
 
@@ -87,11 +86,11 @@ public function __construct($submission) {
 	 * @param $request PKPRequest
 	 */
 	public function setMetadata($request) {
+		$publication = $this->_submission->getCurrentPublication();
 		$this->_package->setCustodian($this->_context->getContactName());
-		$this->_package->setTitle(html_entity_decode($this->_submission->getLocalizedTitle(), ENT_QUOTES, 'UTF-8'));
-		$this->_package->setAbstract(html_entity_decode(strip_tags($this->_submission->getLocalizedAbstract()), ENT_QUOTES, 'UTF-8'));
+		$this->_package->setTitle(html_entity_decode($publication->getLocalizedTitle(), ENT_QUOTES, 'UTF-8'));
+		$this->_package->setAbstract(html_entity_decode(strip_tags($publication->getLocalizedData('abstract')), ENT_QUOTES, 'UTF-8'));
 		$this->_package->setType($this->_section->getLocalizedIdentifyType());
-		$publication = $this->_submission->getCurrentPublication();
 		foreach ($publication->getData('authors') as $author) {
 			$creator = $author->getFullName(true);
 			$affiliation = $author->getLocalizedAffiliation();
@@ -123,7 +122,7 @@ public function _addFile($submissionFile) {
 	 * Add all article galleys to the deposit package.
 	 */
 	public function addGalleys() {
-		foreach ($this->_submission->getGalleys() as $galley) {
+		foreach ($this->_submission->getCurrentPublication()->getData('galleys') as $galley) {
 			$this->_addFile($galley->getFile());
 		}
 	}
diff --git a/templates/authorDepositForm.tpl b/templates/authorDepositForm.tpl
index 860cb2c..90594a0 100644
--- a/templates/authorDepositForm.tpl
+++ b/templates/authorDepositForm.tpl
@@ -45,7 +45,7 @@
 	{csrf}
 
 	{if !empty($depositPoints)}
-		{translate key="plugins.generic.sword.authorDepositDescription" submissionTitle=$submission->getLocalizedTitle()}
+		{translate key="plugins.generic.sword.authorDepositDescription" submissionTitle=$submission->getCurrentPublication()->getLocalizedTitle()}
 		<fieldset id="authorDepositPoints">
 			<ul class="prefabDepositPoints" style="list-style: none;">
 				{foreach from=$depositPoints item=depositPoint key=depositPointKey name="depositPoints"}
@@ -97,7 +97,7 @@
 	{/if}{* !empty($depositPoints) *}
 
 	{if $allowAuthorSpecify}
-		{translate key="plugins.generic.sword.authorCustomDepositDescription" submissionTitle=$submission->getLocalizedTitle()}
+		{translate key="plugins.generic.sword.authorCustomDepositDescription" submissionTitle=$submission->getCurrentPublication()->getLocalizedTitle()}
 		<fieldset class="authorSelfDeposit">
 			<div class="fields">
 				<div class="section">

From b27862725727da72b346d0089d659a4e60d760c0 Mon Sep 17 00:00:00 2001
From: Bozana Bokan <bozana.bokan@posteo.net>
Date: Thu, 19 Dec 2024 11:00:59 +0100
Subject: [PATCH 2/2] after review: fix deprecated functions

---
 AuthorDepositForm.php            | 25 ++++++++++++-------------
 SwordHandler.php                 | 17 +++++++++++------
 classes/DepositPointDAO.php      | 20 +++++++++-----------
 classes/PKPSwordDeposit.php      | 17 +++++++----------
 classes/SwordSchemaMigration.php |  1 -
 5 files changed, 39 insertions(+), 41 deletions(-)

diff --git a/AuthorDepositForm.php b/AuthorDepositForm.php
index c1dba0e..3b2b80c 100644
--- a/AuthorDepositForm.php
+++ b/AuthorDepositForm.php
@@ -15,31 +15,29 @@
 
 use PKP\form\Form;
 
-use APP\plugins\generic\sword\PKPSwordDeposit;
 use APP\plugins\generic\sword\classes\DepositPoint;
 use APP\plugins\generic\sword\classes\DepositPointsHelper;
+use APP\plugins\generic\sword\classes\PKPSwordDeposit;
+use APP\submission\Submission;
+use APP\template\TemplateManager;
+use PKP\context\Context;
+use PKP\db\DAORegistry;
 
 class AuthorDepositForm extends Form {
-	/** @var $_context Context */
+	/** @var Context $_context */
 	protected $_context = null;
 
-	/** @var $_plugin SwordPlugin */
+	/** @var SwordPlugin $_plugin */
 	protected $_plugin = null;
 
-	/** @var $_submission Submission */
+	/** @var Submission $_submission */
 	protected $_submission = null;
 
-	/**
-	 * Constructor
-	 * @param $plugin SwordPlugin
-	 * @param $context Context
-	 * @param $submission Submission
-	 */
+
 	public function __construct(SwordPlugin $plugin, Context $context, Submission $submission) {
 		$this->_plugin = $plugin;
 		$this->_context = $context;
 		$this->_submission = $submission;
-		AppLocale::requireComponents(LOCALE_COMPONENT_PKP_USER);
 		parent::__construct($plugin->getTemplateResource('authorDepositForm.tpl'));
 	}
 
@@ -86,7 +84,7 @@ public function display($request = null, $template = null) {
 	public function execute(...$functionArgs) {
 		parent::execute(...$functionArgs);
 		$request = $functionArgs[0];
-		
+
 		$deposit = new PKPSwordDeposit($this->_submission);
 		$deposit->setMetadata($request);
 		$deposit->addEditorial();
@@ -104,7 +102,7 @@ public function execute(...$functionArgs) {
 			);
 			$deposit->cleanup();
 		}
-		
+
 		$url = '';
 		$depositPoints = $this->getData('depositPoint');
 		$depositableDepositPoints = $this->_getDepositableDepositPoints($this->_context);
@@ -134,6 +132,7 @@ public function execute(...$functionArgs) {
 	 */
 	protected function _getDepositableDepositPoints($context) {
 		$list = [];
+		/** @var DepositPointDAO $depositPointDao */
 		$depositPointDao = DAORegistry::getDAO('DepositPointDAO');
 		$depositPoints = $depositPointDao->getByContextId($context->getId());
 		foreach ($depositPoints as $depositPoint) {
diff --git a/SwordHandler.php b/SwordHandler.php
index 0942652..0e5c120 100644
--- a/SwordHandler.php
+++ b/SwordHandler.php
@@ -13,6 +13,7 @@
 
 namespace APP\plugins\generic\sword;
 
+use APP\facades\Repo;
 use PKP\security\authorization\ContextAccessPolicy;
 use PKP\core\JSONMessage;
 use PKP\plugins\PluginRegistry;
@@ -21,10 +22,12 @@
 use PKP\security\Validation;
 
 use APP\handler\Handler;
-
+use APP\notification\Notification;
+use APP\notification\NotificationManager;
 use APP\plugins\generic\sword\classes\DepositPoint;
 use APP\plugins\generic\sword\classes\DepositPointsHelper;
 use APP\plugins\generic\sword\DepositPointForm;
+use APP\template\TemplateManager;
 
 class SwordHandler extends Handler {
 	/** @var SwordPlugin Sword plugin */
@@ -73,13 +76,14 @@ public function getSwordPlugin() {
 	public function depositPoints($args, $request) {
 		$context = $request->getContext();
 		$depositPointId = $request->getUserVar('depositPointId');
+		/** @var DepositPointDAO $depositPointDao */
 		$depositPointDao = DAORegistry::getDAO('DepositPointDAO');
 		$depositPoint = $depositPointDao->getById($depositPointId, $context->getId());
 		if (!$depositPoint) {
 			return new JSONMessage(false);
 		}
 
-		$isManager = Validation::isAuthorized(ROLE_ID_MANAGER, $context->getId());
+		$isManager = Validation::isAuthorized(Role::ROLE_ID_MANAGER, $context->getId());
 		if (!$isManager && $depositPoint->getType() != SWORD_DEPOSIT_TYPE_OPTIONAL_SELECTION) {
 			return new JSONMessage(false);
 		}
@@ -111,8 +115,7 @@ public function index($args, $request) {
 		$submissionId = (int) array_shift($args);
 		$save = array_shift($args) == 'save';
 
-		$submissionDao = DAORegistry::getDAO('SubmissionDAO');
-		$submission = $submissionDao->getById($submissionId);
+		$submission = Repo::submission()->get($submissionId);
 
 		if (!$submission || !$user || !$context ||
 			($submission->getData('contextId') != $context->getId())) {
@@ -120,8 +123,9 @@ public function index($args, $request) {
 		}
 
 		$userCanDeposit = false;
+		/** @var StageAssignmentDAO $stageAssignmentDao */
 		$stageAssignmentDao = DAORegistry::getDAO('StageAssignmentDAO');
-		$daoResult = $stageAssignmentDao->getBySubmissionAndRoleId($submission->getId(), ROLE_ID_AUTHOR);
+		$daoResult = $stageAssignmentDao->getBySubmissionAndRoleId($submission->getId(), Role::ROLE_ID_AUTHOR);
 		while ($record = $daoResult->next()) {
 			if($user->getId() == $record->getData('userId')) {
 				$userCanDeposit = true;
@@ -143,6 +147,7 @@ public function index($args, $request) {
 					$responses = $authorDepositForm->execute($request);
 					$templateMgr = TemplateManager::getManager($request);
 					$results = [];
+					/** @var DepositPointDAO $depositPointDao */
 					$depositPointDao = DAORegistry::getDAO('DepositPointDAO');
 					$depositPoints = iterator_to_array($depositPointDao->getByContextId($context->getId()));
 					foreach ($responses as $url => $response) {
@@ -168,7 +173,7 @@ public function index($args, $request) {
 					$notificationManager = new NotificationManager();
 					$notificationManager->createTrivialNotification(
 						$user->getId(),
-						NOTIFICATION_TYPE_ERROR,
+						Notification::NOTIFICATION_TYPE_ERROR,
 						['contents' => __('plugins.importexport.sword.depositFailed') . ': ' . $e->getMessage()]
 					);
 					error_log($e->getTraceAsString());
diff --git a/classes/DepositPointDAO.php b/classes/DepositPointDAO.php
index 61ca84f..7b65391 100644
--- a/classes/DepositPointDAO.php
+++ b/classes/DepositPointDAO.php
@@ -22,10 +22,7 @@ class DepositPointDAO extends DAO {
 	/** @var SwordPlugin reference to SWORD plugin */
 	protected $_plugin = null;
 
-	/**
-	 * Constructor
-	 * @param $parentPlugin SwordPlugin
-	 */
+
 	public function __construct(SwordPlugin $parentPlugin) {
 		$this->_plugin = $parentPlugin;
 		parent::__construct();
@@ -48,7 +45,7 @@ public function newDataObject() {
 	public function getById($depositPointId, $contextId = null) {
 		$params = [(int) $depositPointId];
 		if ($contextId) $params[] = (int) $contextId;
-		
+
 		$result = $this->retrieve(
 			'SELECT * FROM deposit_points WHERE deposit_point_id = ? ' . ($contextId?' AND context_id = ?':''),
 			$params
@@ -72,14 +69,14 @@ public function _fromRow($row) {
 		$depositPoint->setSwordUsername($row['sword_username']);
 		$depositPoint->setSwordPassword($row['sword_password']);
 		$depositPoint->setSwordApikey($row['sword_apikey']);
-		
+
 		$this->getDataObjectSettings(
 			'deposit_point_settings',
 			'deposit_point_id',
 			$row['deposit_point_id'],
 			$depositPoint
 		);
-		
+
 		return $depositPoint;
 	}
 
@@ -111,9 +108,9 @@ public function insertObject($depositPoint) {
 			]
 		);
 		$depositPoint->setId($this->getInsertId());
-		
+
 		$this->updateLocaleFields($depositPoint);
-		
+
 		return $depositPoint->getId();
 	}
 
@@ -121,7 +118,8 @@ public function insertObject($depositPoint) {
 	 * Get a list of fields for which localized data is supported
 	 * @return array
 	 */
-	public function getLocaleFieldNames() {
+	public function getLocaleFieldNames(): array
+	{
 		return ['name', 'description'];
 	}
 
@@ -164,7 +162,7 @@ public function updateObject($depositPoint) {
 				$depositPoint->getId()
 			]
 		);
-		
+
 		$this->updateLocaleFields($depositPoint);
 	}
 
diff --git a/classes/PKPSwordDeposit.php b/classes/PKPSwordDeposit.php
index be7fdb1..9c1fc59 100644
--- a/classes/PKPSwordDeposit.php
+++ b/classes/PKPSwordDeposit.php
@@ -15,14 +15,12 @@
 
 namespace APP\plugins\generic\sword\classes;
 
-use PKP\submissionFile\SubmissionFile;
-use PKP\file\FileManager;
-
-use APP\facades\Repo;
 use APP\core\Application;
-use APP\core\Services;
-
+use APP\facades\Repo;
 use APP\plugins\generic\sword\classes\PKPPackagerMetsSwap;
+use Exception;
+use PKP\file\FileManager;
+use PKP\submissionFile\SubmissionFile;
 
 require_once dirname(__FILE__) . '/../libs/swordappv2/swordappclient.php';
 require_once dirname(__FILE__) . '/../libs/swordappv2/swordappentry.php';
@@ -43,7 +41,7 @@ class PKPSwordDeposit {
 	/** @var Issue */
 	protected $_issue = null;
 
-	/** @var Article */
+	/** @var Submission */
 	protected $_submission = null;
 
 	/**
@@ -110,11 +108,10 @@ public function setMetadata($request) {
 	 * @param $submissionFile SubmissionFile
 	 */
 	public function _addFile($submissionFile) {
-		$fileService = Services::get('file');
-		$file = $fileService->get($submissionFile->getData('fileId'));
+		$file = app()->get('file')->get($submissionFile->getData('fileId'));
 		$targetFilename = preg_replace('/[^A-Za-z0-9_\-\.]/', '_', $submissionFile->getLocalizedData('name'));
 		$targetFilePath = $this->_outPath . '/files/' . $targetFilename;
-		file_put_contents($targetFilePath, $fileService->fs->read($file->path));
+		file_put_contents($targetFilePath, app()->get('file')->fs->read($file->path));
 		$this->_package->addFile($targetFilename, $file->mimetype);
 	}
 
diff --git a/classes/SwordSchemaMigration.php b/classes/SwordSchemaMigration.php
index d585f5c..7a3c278 100644
--- a/classes/SwordSchemaMigration.php
+++ b/classes/SwordSchemaMigration.php
@@ -14,7 +14,6 @@
 namespace APP\plugins\generic\sword\classes;
 
 use Illuminate\Database\Migrations\Migration;
-use Illuminate\Database\Schema\Builder;
 use Illuminate\Database\Schema\Blueprint;
 use Illuminate\Support\Facades\Schema;