after review: fix deprecated functions

controllers/grid/pubIds/PubIdExportSubmissionsListGridCellProvider.php

@@ -32,7 +32,7 @@ public function getTemplateVarsFromRowColumn($row, $column)
 
         switch ($columnId) {
             case 'pubId':
-                return ['label' => $submission->getStoredPubId($this->_plugin->getPubIdType())];
+                return ['label' => $submission->getCurrentPublication()->getStoredPubId($this->_plugin->getPubIdType())];
         }
         return parent::getTemplateVarsFromRowColumn($row, $column);
     }

plugins/generic/datacite/filter/DataciteXmlFilter.php

@@ -24,6 +24,9 @@
 use APP\plugins\generic\datacite\DataciteExportPlugin;
 use APP\publication\Publication;
 use APP\submission\Submission;
+use DOMDocument;
+use DOMNode;
+use PKP\context\Context;
 use PKP\core\PKPString;
 use PKP\db\DAORegistry;
 use PKP\facades\Locale;
@@ -87,9 +90,8 @@ public function __construct($filterGroup)
      *
      * @param Issue|Submission|Galley $pubObject
      *
-     * @return \DOMDocument
      */
-    public function &process(&$pubObject)
+    public function &process(&$pubObject): DOMDocument
     {
         // Create the XML document
         $doc = new \DOMDocument('1.0', 'utf-8');
@@ -103,20 +105,22 @@ public function &process(&$pubObject)
         $cache = $plugin->getCache();
 
         // Get all objects
-        $issue = $article = $galley = $galleyFile = null;
+        $issue = $article = $galley = $galleyFile = $doi = null;
         if ($pubObject instanceof Issue) {
             $issue = $pubObject;
             if (!$cache->isCached('issues', $issue->getId())) {
                 $cache->add($issue, null);
             }
+            $doi = $issue->getDoi();
         } elseif ($pubObject instanceof Submission) {
             $article = $pubObject;
             if (!$cache->isCached('articles', $article->getId())) {
                 $cache->add($article, null);
             }
+            $doi = $article->getCurrentPublication()->getDoi();
         } elseif ($pubObject instanceof Galley) {
             $galley = $pubObject;
-            $galleyFile = $galley->getFile();
+            $galleyFile = Repo::submissionFile()->get($galley->getData('submissionFileId'));
             $publication = Repo::publication()->get($galley->getData('publicationId'));
             if ($cache->isCached('articles', $publication->getData('submissionId'))) {
                 $article = $cache->get('articles', $publication->getData('submissionId'));
@@ -138,6 +142,7 @@ public function &process(&$pubObject)
                     }
                 }
             }
+            $doi = $galley->getDoi();
         }
         if (!$issue) {
             $issueId = $article->getCurrentPublication()->getData('issueId');
@@ -174,7 +179,6 @@ public function &process(&$pubObject)
         $rootNode = $this->createRootNode($doc);
         $doc->appendChild($rootNode);
         // DOI (mandatory)
-        $doi = $pubObject->getStoredPubId('doi');
         if ($plugin->isTestMode($context)) {
             $testDOIPrefix = $plugin->getSetting($context->getId(), 'testDOIPrefix');
             assert(!empty($testDOIPrefix));
@@ -264,12 +268,8 @@ public function &process(&$pubObject)
     //
     /**
      * Create and return the root node.
-     *
-     * @param \DOMDocument $doc
-     *
-     * @return \DOMElement
      */
-    public function createRootNode($doc)
+    public function createRootNode(DOMDocument $doc): DOMNode
     {
         /** @var DataciteExportDeployment */
         $deployment = $this->getDeployment();
@@ -281,18 +281,8 @@ public function createRootNode($doc)
 
     /**
      * Create creators node.
-     *
-     * @param \DOMDocument $doc
-     * @param \APP\issue\Issue $issue
-     * @param \APP\publication\Publication $publication
-     * @param \PKP\galley\Galley $galley
-     * @param \PKP\submissionFile\SubmissionFile $galleyFile
-     * @param string $publisher
-     * @param array $objectLocalePrecedence
-     *
-     * @return \DOMElement
      */
-    public function createCreatorsNode($doc, $issue, $publication, $galley, $galleyFile, $publisher, $objectLocalePrecedence)
+    public function createCreatorsNode(DOMDocument $doc, Issue $issue, Publication $publication, Galley $galley, SubmissionFile $galleyFile, string $publisher, array $objectLocalePrecedence): DOMNode
     {
         /** @var DataciteExportDeployment */
         $deployment = $this->getDeployment();
@@ -366,17 +356,8 @@ public function createCreatorsNode($doc, $issue, $publication, $galley, $galleyF
 
     /**
      * Create titles node.
-     *
-     * @param \DOMDocument $doc
-     * @param \APP\issue\Issue $issue
-     * @param \APP\publication\Publication $publication
-     * @param \PKP\galley\Galley $galley
-     * @param \PKP\submissionFile\SubmissionFile $galleyFile
-     * @param array $objectLocalePrecedence
-     *
-     * @return \DOMElement
      */
-    public function createTitlesNode($doc, $issue, $publication, $galley, $galleyFile, $objectLocalePrecedence)
+    public function createTitlesNode(DOMDocument $doc, Issue $issue, Publication $publication, Galley $galley, SubmissionFile $galleyFile, array $objectLocalePrecedence): DOMNode
     {
         /** @var DataciteExportDeployment */
         $deployment = $this->getDeployment();
@@ -419,18 +400,8 @@ public function createTitlesNode($doc, $issue, $publication, $galley, $galleyFil
 
     /**
      * Create a date node list.
-     *
-     * @param \DOMDocument $doc
-     * @param Issue $issue
-     * @param Submission $article
-     * @param Publication $publication
-     * @param Galley $galley
-     * @param SubmissionFile $galleyFile
-     * @param string $publicationDate
-     *
-     * @return \DOMElement
      */
-    public function createDatesNode($doc, $issue, $article, $publication, $galley, $galleyFile, $publicationDate)
+    public function createDatesNode(DOMDocument $doc, Issue $issue, Submission $article, Publication $publication, Galley $galley, SubmissionFile $galleyFile, string $publicationDate): DOMNode
     {
         /** @var DataciteExportDeployment */
         $deployment = $this->getDeployment();
@@ -508,16 +479,8 @@ public function createDatesNode($doc, $issue, $article, $publication, $galley, $
 
     /**
      * Create a resource type node.
-     *
-     * @param \DOMDocument $doc
-     * @param Issue $issue
-     * @param Submission $article
-     * @param Galley $galley
-     * @param SubmissionFile $galleyFile
-     *
-     * @return \DOMElement
      */
-    public function createResourceTypeNode($doc, $issue, $article, $galley, $galleyFile)
+    public function createResourceTypeNode(DOMDocument $doc, Issue $issue, Submission $article, Galley $galley, SubmissionFile $galleyFile): DOMNode
     {
         /** @var DataciteExportDeployment */
         $deployment = $this->getDeployment();
@@ -561,15 +524,8 @@ public function createResourceTypeNode($doc, $issue, $article, $galley, $galleyF
 
     /**
      * Generate alternate identifiers node list.
-     *
-     * @param \DOMDocument $doc
-     * @param Issue $issue
-     * @param Submission $article
-     * @param Galley $galley
-     *
-     * @return \DOMElement
      */
-    public function createAlternateIdentifiersNode($doc, $issue, $article, $galley)
+    public function createAlternateIdentifiersNode(DOMDocument $doc, Issue $issue, Submission $article, Galley $galley): DOMNode
     {
         $deployment = $this->getDeployment();
         $context = $deployment->getContext();
@@ -605,24 +561,16 @@ public function createAlternateIdentifiersNode($doc, $issue, $article, $galley)
 
     /**
      * Generate related identifiers node list.
-     *
-     * @param \DOMDocument $doc
-     * @param Issue $issue
-     * @param Submission $article
-     * @param Publication $publication
-     * @param Galley $galley
-     *
-     * @return ?\DOMElement
      */
-    public function createRelatedIdentifiersNode($doc, $issue, $article, $publication, $galley)
+    public function createRelatedIdentifiersNode(DOMDocument $doc, Issue $issue, Submission $article, Publication $publication, Galley $galley): ?DOMNode
     {
         $deployment = $this->getDeployment();
         $relatedIdentifiersNode = $doc->createElementNS($deployment->getNamespace(), 'relatedIdentifiers');
         switch (true) {
             case isset($galley):
                 // Part of: article.
                 assert(isset($article));
-                $doi = $article->getStoredPubId('doi');
+                $doi = $publication->getStoredPubId('doi');
                 if (!empty($doi)) {
                     $relatedIdentifiersNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'relatedIdentifier', htmlspecialchars($doi, ENT_COMPAT, 'UTF-8')));
                     $node->setAttribute('relatedIdentifierType', DATACITE_IDTYPE_DOI);
@@ -679,17 +627,8 @@ public function createRelatedIdentifiersNode($doc, $issue, $article, $publicatio
 
     /**
      * Create a sizes node list.
-     *
-     * @param \DOMDocument $doc
-     * @param Issue $issue
-     * @param Submission $article
-     * @param Publication $publication
-     * @param Galley $galley
-     * @param SubmissionFile $galleyFile
-     *
-     * @return ?\DOMElement Can be null if a size cannot be identified for the given object.
      */
-    public function createSizesNode($doc, $issue, $article, $publication, $galley, $galleyFile)
+    public function createSizesNode(DOMDocument $doc, Issue $issue, Submission $article, Publication $publication, Galley $galley, SubmissionFile $galleyFile): ?DOMNode
     {
         $deployment = $this->getDeployment();
         $sizes = [];
@@ -726,18 +665,8 @@ public function createSizesNode($doc, $issue, $article, $publication, $galley, $
 
     /**
      * Create descriptions node list.
-     *
-     * @param \DOMDocument $doc
-     * @param Issue $issue
-     * @param Submission $article
-     * @param Publication $publication
-     * @param Galley $galley
-     * @param SubmissionFile $galleyFile
-     * @param array $objectLocalePrecedence
-     *
-     * @return ?\DOMElement Can be null if a size cannot be identified for the given object.
      */
-    public function createDescriptionsNode($doc, $issue, $article, $publication, $galley, $galleyFile, $objectLocalePrecedence)
+    public function createDescriptionsNode(DOMDocument $doc, Issue $issue, Submission $article, Publication $publication, Galley $galley, SubmissionFile $galleyFile, array $objectLocalePrecedence): ?DOMNode
     {
         /** @var DataciteExportDeployment */
         $deployment = $this->getDeployment();
@@ -785,17 +714,8 @@ public function createDescriptionsNode($doc, $issue, $article, $publication, $ga
 
     /**
      * Create related items node.
-     *
-     * @param \DOMDocument $doc
-     * @param Issue $issue
-     * @param Submission $article
-     * @param Publication $publication
-     * @param string $publisher
-     * @param array $objectLocalePrecedence
-     *
-     * @return ?\DOMElement Can be null if a size cannot be identified for the given object.
      */
-    public function createRelatedItemsNode($doc, $issue, $article, $publication, $publisher, $objectLocalePrecedence)
+    public function createRelatedItemsNode(DOMDocument $doc, Issue $issue, Submission $article, Publication $publication, string $publisher, array $objectLocalePrecedence): ?DOMNode
     {
         /** @var DataciteExportDeployment */
         $deployment = $this->getDeployment();
@@ -878,15 +798,9 @@ public function createRelatedItemsNode($doc, $issue, $article, $publication, $pu
     /**
      * Identify the locale precedence for this export.
      *
-     * @param \PKP\context\Context $context
-     * @param \APP\submission\Submission $article
-     * @param \APP\publication\Publication $publication
-     * @param \PKP\galley\Galley $galley
-     *
-     * @return array A list of valid PKP locales in descending
-     *  order of priority.
+     * @return array A list of valid PKP locales ordered by priority.
      */
-    public function getObjectLocalePrecedence($context, $article, $publication, $galley)
+    public function getObjectLocalePrecedence(Context $context, Submission $article, Publication $publication, Galley $galley): array
     {
         $locales = [];
         if ($galley instanceof Galley && Locale::isLocaleValid($galley->getLocale())) {
@@ -947,10 +861,10 @@ public function translateLanguageToLocale($language)
      * @param array $localePrecedence An array of locales
      *  by descending priority.
      *
-     * @return mixed|null The value of the primary locale
+     * @return mixed The value of the primary locale
      *  or null if no primary translation could be found.
      */
-    public function getPrimaryTranslation($localizedData, $localePrecedence)
+    public function getPrimaryTranslation(array $localizedData, array $localePrecedence): mixed
     {
         // Check whether we have localized data at all.
         if (!is_array($localizedData) || empty($localizedData)) {
@@ -984,7 +898,7 @@ public function getPrimaryTranslation($localizedData, $localePrecedence)
      *
      * @return array Re-ordered localized data.
      */
-    public function getTranslationsByPrecedence($localizedData, $localePrecedence)
+    public function getTranslationsByPrecedence(array $localizedData, array $localePrecedence): array
     {
         $reorderedLocalizedData = [];
 
@@ -1013,13 +927,10 @@ public function getTranslationsByPrecedence($localizedData, $localePrecedence)
      * Construct an issue title from the journal title
      * and the issue identification.
      *
-     * @param \APP\issue\Issue $issue
-     * @param array $objectLocalePrecedence
-     *
      * @return array|string An array of localized issue titles
      *  or a string if a locale has been given.
      */
-    public function getIssueInformation($issue, $objectLocalePrecedence = null)
+    public function getIssueInformation(Issue $issue, array $objectLocalePrecedence = null): array|string
     {
         $deployment = $this->getDeployment();
         $context = $deployment->getContext();
@@ -1042,13 +953,8 @@ public function getIssueInformation($issue, $objectLocalePrecedence = null)
 
     /**
      * Construct a table of content for an issue.
-     *
-     * @param \APP\issue\Issue $issue
-     * @param array $objectLocalePrecedence
-     *
-     * @return string
      */
-    public function getIssueToc($issue, $objectLocalePrecedence)
+    public function getIssueToc(Issue $issue, array $objectLocalePrecedence): string
     {
         $submissions = Repo::submission()
             ->getCollector()

plugins/metadata/dc11/filter/Dc11SchemaArticleAdapter.php

@@ -199,7 +199,7 @@ public function &extractMetadataFromDataObject(&$article)
             if ($issue && $pubIssueId = $issue->getStoredPubId($publicIdentifier)) {
                 $dc11Description->addStatement('dc:source', $pubIssueId, MetadataDescription::METADATA_DESCRIPTION_UNKNOWN_LOCALE);
             }
-            if ($pubArticleId = $article->getStoredPubId($publicIdentifier)) {
+            if ($pubArticleId = $publication->getStoredPubId($publicIdentifier)) {
                 $dc11Description->addStatement('dc:identifier', $pubArticleId);
             }
             foreach ($galleys as $galley) {

plugins/reports/articles/ArticleReportPlugin.php

@@ -193,9 +193,9 @@ public function display($args, $request)
                 'agencies' => join(', ', $agencies[Locale::getLocale()] ?? $agencies[$submission->getData('locale')] ?? []),
                 'status' => $submission->getData('status') == PKPSubmission::STATUS_QUEUED ? $this->getStageLabel($submission->getData('stageId')) : __($statusMap[$submission->getData('status')]),
                 'url' => $request->url(null, 'workflow', 'access', $submission->getId()),
-                'doi' => $submission->getStoredPubId('doi'),
+                'doi' => $publication->getDoi(),
                 'dateSubmitted' => $submission->getData('dateSubmitted'),
-                'lastModified' => $submission->getLastModified(),
+                'lastModified' => $submission->getData('lastModified'),
                 'firstPublished' => $submission->getOriginalPublication()?->getData('datePublished') ?? '',
                 'editors' => $editors,
                 'decisions' => $editDecisions->toArray(),

templates/frontend/objects/article_details.tpl

@@ -410,7 +410,7 @@
 				{if $pubIdPlugin->getPubIdType() == 'doi'}
 					{continue}
 				{/if}
-				{assign var=pubId value=$article->getStoredPubId($pubIdPlugin->getPubIdType())}
+				{assign var=pubId value=$publication->getStoredPubId($pubIdPlugin->getPubIdType())}
 				{if $pubId}
 					<section class="item pubid">
 						<h2 class="label">