pkp · touhidurabir · Aug 16, 2024 · Aug 16, 2024 · Aug 19, 2024 · Aug 20, 2024
diff --git a/classes/search/ArticleSearch.php b/classes/search/ArticleSearch.php
@@ -23,6 +23,7 @@
 use APP\core\Request;
 use APP\facades\Repo;
 use APP\issue\IssueAction;
+use PKP\controlledVocab\ControlledVocab;
 use PKP\db\DAORegistry;
 use PKP\facades\Locale;
 use PKP\plugins\Hook;
@@ -199,7 +200,7 @@ public function getSearchFilters($request)
                 $context = $contextDao->getById($searchFilters['searchJournal']);
             } elseif (array_key_exists('journalTitle', $request->getUserVars())) {
                 $contexts = $contextDao->getAll(true);
-                while ($context = $contexts->next()) {
+                while ($context = $contexts->next()) { /** @var \PKP\context\Context $context */
                     if (in_array(
                         $request->getUserVar('journalTitle'),
                         (array) $context->getName(null)
@@ -333,8 +334,14 @@ public function getSimilarityTerms($submissionId)
             $article = Repo::submission()->get($submissionId);
             if ($article->getData('status') === PKPSubmission::STATUS_PUBLISHED) {
                 // Retrieve keywords (if any).
-                $submissionSubjectDao = DAORegistry::getDAO('SubmissionKeywordDAO'); /** @var \PKP\submission\SubmissionKeywordDAO $submissionSubjectDao */
-                $allSearchTerms = array_filter($submissionSubjectDao->getKeywords($article->getCurrentPublication()->getId(), [Locale::getLocale(), $article->getData('locale'), Locale::getPrimaryLocale()]));
+                $allSearchTerms = array_filter(
+                    Repo::controlledVocab()->getBySymbolic(
+                        ControlledVocab::CONTROLLED_VOCAB_SUBMISSION_KEYWORD,
+                        Application::ASSOC_TYPE_PUBLICATION,
+                        $article->getCurrentPublication()->getId(),
+                        [Locale::getLocale(), $article->getData('locale'), Locale::getPrimaryLocale()]
+                    )
+                );
                 foreach ($allSearchTerms as $locale => $localeSearchTerms) {
                     $searchTerms += $localeSearchTerms;
                 }

diff --git a/lib/pkp b/lib/pkp
diff --git a/plugins/generic/citationStyleLanguage b/plugins/generic/citationStyleLanguage
diff --git a/plugins/importexport/doaj/filter/DOAJJsonFilter.php b/plugins/importexport/doaj/filter/DOAJJsonFilter.php
@@ -20,10 +20,9 @@
 use APP\facades\Repo;
 use APP\plugins\importexport\doaj\DOAJExportDeployment;
 use APP\plugins\importexport\doaj\DOAJExportPlugin;
+use PKP\controlledVocab\ControlledVocab;
 use PKP\core\PKPString;
-use PKP\db\DAORegistry;
 use PKP\plugins\importexport\PKPImportExportFilter;
-use PKP\submission\SubmissionKeywordDAO;
 
 class DOAJJsonFilter extends PKPImportExportFilter
 {
@@ -176,9 +175,13 @@ public function &process(&$pubObject)
             $article['bibjson']['abstract'] = PKPString::html2text($abstract);
         }
         // Keywords
-        /** @var SubmissionKeywordDAO */
-        $dao = DAORegistry::getDAO('SubmissionKeywordDAO');
-        $keywords = $dao->getKeywords($publication->getId(), [$publicationLocale]);
+        $keywords = Repo::controlledVocab()->getBySymbolic(
+            ControlledVocab::CONTROLLED_VOCAB_SUBMISSION_KEYWORD,
+            Application::ASSOC_TYPE_PUBLICATION,
+            $publication->getId(),
+            [$publicationLocale]
+        );
+
         $allowedNoOfKeywords = array_slice($keywords[$publicationLocale] ?? [], 0, 6);
         if (!empty($keywords[$publicationLocale])) {
             $article['bibjson']['keywords'] = $allowedNoOfKeywords;

diff --git a/plugins/importexport/doaj/filter/DOAJXmlFilter.php b/plugins/importexport/doaj/filter/DOAJXmlFilter.php
@@ -20,10 +20,9 @@
 use APP\plugins\importexport\doaj\DOAJExportPlugin;
 use APP\publication\Publication;
 use APP\submission\Submission;
+use PKP\controlledVocab\ControlledVocab;
 use PKP\core\PKPString;
-use PKP\db\DAORegistry;
 use PKP\i18n\LocaleConversion;
-use PKP\submission\SubmissionKeywordDAO;
 
 class DOAJXmlFilter extends \PKP\plugins\importexport\native\filter\NativeExportFilter
 {
@@ -189,16 +188,22 @@ public function &process(&$pubObjects)
             $request = Application::get()->getRequest();
             $recordNode->appendChild($node = $doc->createElement('fullTextUrl', htmlspecialchars($request->getDispatcher()->url($request, Application::ROUTE_PAGE, null, 'article', 'view', [$pubObject->getId()], urlLocaleForPage: ''), ENT_COMPAT, 'UTF-8')));
             $node->setAttribute('format', 'html');
+
             // Keywords
             $supportedLocales = $context->getSupportedFormLocales();
-            /** @var SubmissionKeywordDAO */
-            $dao = DAORegistry::getDAO('SubmissionKeywordDAO');
-            $articleKeywords = $dao->getKeywords($publication->getId(), $supportedLocales);
+            $articleKeywords = Repo::controlledVocab()->getBySymbolic(
+                ControlledVocab::CONTROLLED_VOCAB_SUBMISSION_KEYWORD,
+                Application::ASSOC_TYPE_PUBLICATION,
+                $publication->getId(),
+                $supportedLocales
+            );
+
             if (array_key_exists($publication->getData('locale'), $articleKeywords)) {
                 $keywordsInArticleLocale = $articleKeywords[$publication->getData('locale')];
                 unset($articleKeywords[$publication->getData('locale')]);
                 $articleKeywords = array_merge([$publication->getData('locale') => $keywordsInArticleLocale], $articleKeywords);
             }
+
             foreach ($articleKeywords as $locale => $keywords) {
                 $keywordsNode = $doc->createElement('keywords');
                 $keywordsNode->setAttribute('language', LocaleConversion::get3LetterIsoFromLocale($locale));

diff --git a/plugins/metadata/dc11/filter/Dc11SchemaArticleAdapter.php b/plugins/metadata/dc11/filter/Dc11SchemaArticleAdapter.php
@@ -28,15 +28,14 @@
 use APP\oai\ojs\OAIDAO;
 use APP\plugins\PubIdPlugin;
 use APP\submission\Submission;
+use PKP\controlledVocab\ControlledVocab;
 use PKP\core\PKPApplication;
 use PKP\db\DAORegistry;
 use PKP\facades\Locale;
 use PKP\metadata\MetadataDataObjectAdapter;
 use PKP\metadata\MetadataDescription;
 use PKP\plugins\Hook;
 use PKP\plugins\PluginRegistry;
-use PKP\submission\SubmissionKeywordDAO;
-use PKP\submission\SubmissionSubjectDAO;
 
 class Dc11SchemaArticleAdapter extends MetadataDataObjectAdapter
 {
@@ -90,12 +89,20 @@ public function &extractMetadataFromDataObject(&$article)
         }
 
         // Subject
-        $submissionKeywordDao = DAORegistry::getDAO('SubmissionKeywordDAO'); /** @var SubmissionKeywordDAO $submissionKeywordDao */
-        $submissionSubjectDao = DAORegistry::getDAO('SubmissionSubjectDAO'); /** @var SubmissionSubjectDAO $submissionSubjectDao */
         $supportedLocales = $journal->getSupportedFormLocales();
         $subjects = array_merge_recursive(
-            (array) $submissionKeywordDao->getKeywords($publication->getId(), $supportedLocales),
-            (array) $submissionSubjectDao->getSubjects($publication->getId(), $supportedLocales)
+            Repo::controlledVocab()->getBySymbolic(
+                ControlledVocab::CONTROLLED_VOCAB_SUBMISSION_KEYWORD,
+                Application::ASSOC_TYPE_PUBLICATION,
+                $publication->getId(),
+                $supportedLocales
+            ),
+            Repo::controlledVocab()->getBySymbolic(
+                ControlledVocab::CONTROLLED_VOCAB_SUBMISSION_SUBJECT,
+                Application::ASSOC_TYPE_PUBLICATION,
+                $publication->getId(),
+                $supportedLocales
+            )
         );
         $this->_addLocalizedElements($dc11Description, 'dc:subject', $subjects);
 

diff --git a/plugins/oaiMetadataFormats/dc/tests/OAIMetadataFormat_DCTest.php b/plugins/oaiMetadataFormats/dc/tests/OAIMetadataFormat_DCTest.php
@@ -35,18 +35,18 @@
 use APP\section\Section;
 use APP\submission\Submission;
 use Illuminate\Support\LazyCollection;
+use Mockery;
 use PHPUnit\Framework\Attributes\CoversClass;
 use PHPUnit\Framework\MockObject\MockObject;
 use PKP\author\Repository as AuthorRepository;
+use PKP\controlledVocab\Repository as ControlledVocabRepository;
 use PKP\core\Dispatcher;
 use PKP\core\Registry;
 use PKP\db\DAORegistry;
 use PKP\doi\Doi;
 use PKP\galley\Collector as GalleyCollector;
 use PKP\galley\Galley;
 use PKP\oai\OAIRecord;
-use PKP\submission\SubmissionKeywordDAO;
-use PKP\submission\SubmissionSubjectDAO;
 use PKP\tests\PKPTestCase;
 
 #[CoversClass(OAIMetadataFormat_DC::class)]
@@ -58,7 +58,7 @@ class OAIMetadataFormat_DCTest extends PKPTestCase
      */
     protected function getMockedDAOs(): array
     {
-        return [...parent::getMockedDAOs(), 'OAIDAO', 'SubmissionSubjectDAO', 'SubmissionKeywordDAO'];
+        return [...parent::getMockedDAOs(), 'OAIDAO'];
     }
 
     /**
@@ -79,6 +79,19 @@ protected function getMockedContainerKeys(): array
 
     public function testToXml()
     {
+        $controlledVocabRepoMock = Mockery::mock(ControlledVocabRepository::class)
+            ->makePartial()
+            ->shouldReceive('getBySymbolic')
+            ->twice()
+            ->withAnyArgs()
+            ->andReturn(
+                ['en' => ['article-keyword']],
+                ['en' => ['article-subject', 'article-subject-class']]
+            )
+            ->getMock();
+
+        app()->instance(ControlledVocabRepository::class, $controlledVocabRepoMock);
+
         //
         // Create test data.
         //
@@ -102,6 +115,7 @@ public function testToXml()
         $publication = $this->getMockBuilder(Publication::class)
             ->onlyMethods([])
             ->getMock();
+        $publication->setData('id', 0);
         $publication->setData('issueId', 96);
         $publication->setData('pages', 15);
         $publication->setData('type', 'art-type', 'en');
@@ -167,6 +181,7 @@ public function testToXml()
             ->willReturn(Journal::PUBLISHING_MODE_OPEN);
         $journal->setName('journal-title', 'en');
         $journal->setData('publisherInstitution', 'journal-publisher');
+        $journal->setData('supportedFormLocales', []);
         $journal->setPrimaryLocale('en');
         $journal->setPath('journal-path');
         $journal->setData('onlineIssn', 'onlineIssn');
@@ -263,25 +278,6 @@ public function testToXml()
             ->willReturn(LazyCollection::wrap($galleys));
         app()->instance(GalleyCollector::class, $mockGalleyCollector);
 
-        // Mocked DAO to return the subjects
-        $submissionSubjectDao = $this->getMockBuilder(SubmissionSubjectDAO::class)
-            ->onlyMethods(['getSubjects'])
-            ->getMock();
-        $submissionSubjectDao->expects($this->any())
-            ->method('getSubjects')
-            ->willReturn(['en' => ['article-subject', 'article-subject-class']]);
-        DAORegistry::registerDAO('SubmissionSubjectDAO', $submissionSubjectDao);
-
-        // Mocked DAO to return the keywords
-        $submissionKeywordDao = $this->getMockBuilder(SubmissionKeywordDAO::class)
-            ->onlyMethods(['getKeywords'])
-            ->getMock();
-        $submissionKeywordDao->expects($this->any())
-            ->method('getKeywords')
-            ->willReturn(['en' => ['article-keyword']]);
-        DAORegistry::registerDAO('SubmissionKeywordDAO', $submissionKeywordDao);
-
-
         //
         // Test
         //

diff --git a/plugins/oaiMetadataFormats/rfc1807/OAIMetadataFormat_RFC1807.php b/plugins/oaiMetadataFormats/rfc1807/OAIMetadataFormat_RFC1807.php
@@ -17,12 +17,11 @@
 namespace APP\plugins\oaiMetadataFormats\rfc1807;
 
 use APP\core\Application;
+use APP\facades\Repo;
 use APP\issue\IssueAction;
-use PKP\db\DAORegistry;
+use PKP\controlledVocab\ControlledVocab;
 use PKP\oai\OAIMetadataFormat;
 use PKP\oai\OAIUtils;
-use PKP\submission\SubmissionKeywordDAO;
-use PKP\submission\SubmissionSubjectDAO;
 
 class OAIMetadataFormat_RFC1807 extends OAIMetadataFormat
 {
@@ -68,11 +67,19 @@ public function toXml($record, $format = null)
 
         // Subject
         $supportedLocales = $journal->getSupportedFormLocales();
-        $submissionKeywordDao = DAORegistry::getDAO('SubmissionKeywordDAO'); /** @var SubmissionKeywordDAO $submissionKeywordDao */
-        $submissionSubjectDao = DAORegistry::getDAO('SubmissionSubjectDAO'); /** @var SubmissionSubjectDAO $submissionSubjectDao */
         $subjects = array_merge_recursive(
-            (array) $submissionKeywordDao->getKeywords($publication->getId(), $supportedLocales),
-            (array) $submissionSubjectDao->getSubjects($article->getCurrentPublication()->getId(), $supportedLocales)
+            Repo::controlledVocab()->getBySymbolic(
+                ControlledVocab::CONTROLLED_VOCAB_SUBMISSION_KEYWORD,
+                Application::ASSOC_TYPE_PUBLICATION,
+                $publication->getId(),
+                $supportedLocales
+            ),
+            Repo::controlledVocab()->getBySymbolic(
+                ControlledVocab::CONTROLLED_VOCAB_SUBMISSION_SUBJECT,
+                Application::ASSOC_TYPE_PUBLICATION,
+                $article->getCurrentPublication()->getId(),
+                $supportedLocales
+            )
         );
         $subject = $subjects[$journal->getPrimaryLocale()] ?? '';
 

diff --git a/plugins/reports/articles/ArticleReportPlugin.php b/plugins/reports/articles/ArticleReportPlugin.php
@@ -16,18 +16,15 @@
 
 namespace APP\plugins\reports\articles;
 
+use APP\core\Application;
 use APP\decision\Decision;
 use APP\facades\Repo;
-use PKP\db\DAORegistry;
+use PKP\controlledVocab\ControlledVocab;
 use PKP\facades\Locale;
 use PKP\plugins\ReportPlugin;
 use PKP\security\Role;
 use PKP\stageAssignment\StageAssignment;
 use PKP\submission\PKPSubmission;
-use PKP\submission\SubmissionAgencyDAO;
-use PKP\submission\SubmissionDisciplineDAO;
-use PKP\submission\SubmissionKeywordDAO;
-use PKP\submission\SubmissionSubjectDAO;
 
 class ArticleReportPlugin extends ReportPlugin
 {
@@ -85,11 +82,6 @@ public function display($args, $request)
         // Add BOM (byte order mark) to fix UTF-8 in Excel
         fprintf($fp, chr(0xEF) . chr(0xBB) . chr(0xBF));
 
-        $submissionKeywordDao = DAORegistry::getDAO('SubmissionKeywordDAO'); /** @var SubmissionKeywordDAO $submissionKeywordDao */
-        $submissionSubjectDao = DAORegistry::getDAO('SubmissionSubjectDAO'); /** @var SubmissionSubjectDAO $submissionSubjectDao */
-        $submissionDisciplineDao = DAORegistry::getDAO('SubmissionDisciplineDAO'); /** @var SubmissionDisciplineDAO $submissionDisciplineDao */
-        $submissionAgencyDao = DAORegistry::getDAO('SubmissionAgencyDAO'); /** @var SubmissionAgencyDAO $submissionAgencyDao */
-
         $userGroups = Repo::userGroup()->getCollector()
             ->filterByContextIds([$context->getId()])
             ->getMany()
@@ -159,10 +151,29 @@ public function display($args, $request)
                 $sectionTitles[$sectionId] = $section->getLocalizedTitle();
             }
 
-            $subjects = $submissionSubjectDao->getSubjects($submission->getCurrentPublication()->getId());
-            $disciplines = $submissionDisciplineDao->getDisciplines($submission->getCurrentPublication()->getId());
-            $keywords = $submissionKeywordDao->getKeywords($submission->getCurrentPublication()->getId());
-            $agencies = $submissionAgencyDao->getAgencies($submission->getCurrentPublication()->getId());
+            $subjects = Repo::controlledVocab()->getBySymbolic(
+                ControlledVocab::CONTROLLED_VOCAB_SUBMISSION_SUBJECT,
+                Application::ASSOC_TYPE_PUBLICATION,
+                $submission->getCurrentPublication()->getId()
+            );
+
+            $disciplines = Repo::controlledVocab()->getBySymbolic(
+                ControlledVocab::CONTROLLED_VOCAB_SUBMISSION_DISCIPLINE,
+                Application::ASSOC_TYPE_PUBLICATION,
+                $submission->getCurrentPublication()->getId()
+            );
+
+            $keywords = Repo::controlledVocab()->getBySymbolic(
+                ControlledVocab::CONTROLLED_VOCAB_SUBMISSION_KEYWORD,
+                Application::ASSOC_TYPE_PUBLICATION,
+                $submission->getCurrentPublication()->getId()
+            );
+
+            $agencies = Repo::controlledVocab()->getBySymbolic(
+                ControlledVocab::CONTROLLED_VOCAB_SUBMISSION_AGENCY,
+                Application::ASSOC_TYPE_PUBLICATION,
+                $submission->getCurrentPublication()->getId()
+            );
 
             // Store the submission results
             $results[] = [