pkp/pkp-lib#7505 Support for JATS files/content added

pkp · Dec 7, 2023 · 01087dd · 01087dd
1 parent fb77e91
commit 01087dd
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Showing 4 changed files with 62 additions and 40 deletions.
diff --git a/JatsTemplatePlugin.php b/JatsTemplatePlugin.php
@@ -12,19 +12,11 @@
 
 namespace APP\plugins\generic\jatsTemplate;
 
-use APP\facades\Repo;
-use APP\core\Services;
 use APP\core\Application;
 use APP\plugins\generic\jatsTemplate\classes\Article;
 use APP\template\TemplateManager;
-use PKP\core\PKPString;
-use PKP\db\DAORegistry;
 use PKP\plugins\GenericPlugin;
 use PKP\plugins\Hook;
-use PKP\plugins\PluginRegistry;
-use PKP\search\SearchFileParser;
-use PKP\submissionFile\SubmissionFile;
-use PKP\config\Config;
 
 class JatsTemplatePlugin extends GenericPlugin {
 
@@ -68,7 +60,8 @@ public function callbackFindJats($hookName, $args) {
 		$doc =& $args[3];
 
 		if (!$doc && empty($candidateFiles)) {
-            $doc = new Article($record);
+			$doc = new Article();
+			$doc->convertOAIToXml($record);
 		}
 
 		return false;

diff --git a/classes/Article.php b/classes/Article.php
@@ -14,21 +14,25 @@
 namespace APP\plugins\generic\jatsTemplate\classes;
 
 use APP\core\Application;
-use DOMException;
+use APP\issue\Issue;
+use APP\publication\Publication;
+use APP\section\Section;
+use APP\submission\Submission;
+use PKP\context\Context;
+use PKP\core\PKPRequest;
+use PKP\oai\OAIRecord;
 
 class Article extends \DOMDocument
 {
-    function __construct($record)
+    function __construct()
     {
         parent::__construct('1.0', 'UTF-8');
-        $this->convertToXml($record);
     }
 
     /**
-     * @param $record
-     * @return bool|\DOMDocument
+     * 
      */
-    public function convertToXml($record) :bool|\DOMDocument
+    public function convertOAIToXml(OAIRecord $record): void
     {
         $submission = $record->getData('article');
         $journal = $record->getData('journal');
@@ -37,25 +41,30 @@ public function convertToXml($record) :bool|\DOMDocument
         $publication = $submission->getCurrentPublication();
         $request = Application::get()->getRequest();
 
+        $this->convertSubmission($submission, $journal, $section, $issue, $publication, $request);
+    }
+
+    /**
+     * Convert submission metadata to JATS XML 
+     */
+    public function convertSubmission(Submission $submission, Context $context, Section $section, ?Issue $issue = null, ?Publication $publication = null, PKPRequest $request): void
+    {
         $articleElement = $this->appendChild($this->createElement('article'))
-                ->setAttribute('xmlns:xlink','http://www.w3.org/1999/xlink')->parentNode
-                ->setAttribute('xml:lang', substr($submission->getLocale(), 0, 2))->parentNode
-                ->setAttribute('xmlns:mml','http://www.w3.org/1998/Math/MathML')->parentNode
-                ->setAttribute('xmlns:xsi','http://www.w3.org/2001/XMLSchema-instance')->parentNode;
+            ->setAttribute('xmlns:xlink','http://www.w3.org/1999/xlink')->parentNode
+            ->setAttribute('xml:lang', substr($submission->getLocale(), 0, 2))->parentNode
+            ->setAttribute('xmlns:mml','http://www.w3.org/1998/Math/MathML')->parentNode
+            ->setAttribute('xmlns:xsi','http://www.w3.org/2001/XMLSchema-instance')->parentNode;
 
         $articleFront = new ArticleFront();
-        $articleElement->appendChild($this->importNode($articleFront->create($journal, $submission, $section, $issue, $request, $this), true));
+        $articleElement->appendChild($this->importNode($articleFront->create($context, $submission, $section, $issue, $request, $this, $publication), true));
 
         $articleBody = new ArticleBody();
         $articleElement->appendChild($this->importNode($articleBody->create($submission), true));
 
         $articleBack = new ArticleBack();
         $articleElement->appendChild($this->importNode($articleBack->create($publication), true));
-
-        return $this->loadXml($this->saveXML($articleElement));
     }
 
-
     /**
      * Map the specific HTML tags in title/ sub title for JATS schema compability
      * @see https://jats.nlm.nih.gov/publishing/0.4/xsd/JATS-journalpublishing0.xsd
@@ -76,4 +85,5 @@ public function mapHtmlTagsForTitle(string $htmlTitle): string
 
         return str_replace(array_keys($mappings), array_values($mappings), $htmlTitle);
     }
+
 }
diff --git a/classes/ArticleFront.php b/classes/ArticleFront.php
@@ -19,6 +19,7 @@
 use APP\section\Section;
 use APP\submission\Submission;
 use APP\publication\Publication;
+use PKP\core\PKPApplication;
 use PKP\core\PKPString;
 use PKP\db\DAORegistry;
 use PKP\plugins\PluginRegistry;
@@ -27,16 +28,15 @@
 
 class ArticleFront extends \DOMDocument
 {
-
     /**
      * Create article front element
      */
-    public function create(Journal $journal, Submission $submission, Section $section,Issue $issue, PKPRequest $request, Article $article): \DOMNode
+    public function create(Journal $journal, Submission $submission, Section $section, ?Issue $issue, PKPRequest $request, Article $article, ?Publication $workingPublication = null): \DOMNode
     {
         return $this->appendChild($this->createElement('front'))
             ->appendChild($this->createJournalMeta($journal, $request))
             ->parentNode
-            ->appendChild($this->createArticleMeta($submission, $journal, $section, $issue, $request, $article))
+            ->appendChild($this->createArticleMeta($submission, $journal, $section, $issue, $request, $article, $workingPublication))
             ->parentNode;
     }
 
@@ -87,9 +87,14 @@ public function createJournalMeta(Journal $journal, PKPRequest $request): \DOMNo
                 ->appendChild($this->createTextNode($journal->getSetting('printIssn')))->parentNode
                 ->setAttribute('pub-type','ppub');
         }
+
+        $router = $request->getRouter();
+        $dispatcher = $router->getDispatcher();
+
+        $journalUrl = $dispatcher->url($request, PKPApplication::ROUTE_PAGE, $journal->getPath());
         $journalMetaElement
             ->appendChild($this->createElement('self-uri'))
-            ->setAttribute('xlink:href', $request->url($journal->getPath()));
+            ->setAttribute('xlink:href', $journalUrl);
 
         return $journalMetaElement;
 
@@ -124,9 +129,12 @@ public function createJournalMetaJournalTitleGroup(Journal $journal): \DOMNode
     /**
      * Create xml article-meta DOMNode
      */
-    function createArticleMeta(Submission $submission, Journal $journal, Section $section, Issue $issue, $request, Article $article)
+    function createArticleMeta(Submission $submission, Journal $journal, Section $section, ?Issue $issue, $request, Article $article, ?Publication $workingPublication = null)
     {
         $publication = $submission->getCurrentPublication();
+        if ($workingPublication) {
+            $publication = $workingPublication;
+        }
 
         $articleMetaElement = $this->appendChild($this->createElement('article-meta'));
 
@@ -186,11 +194,16 @@ function createArticleMeta(Submission $submission, Journal $journal, Section $se
         }
 
         $datePublished = $submission->getDatePublished();
-        if (!$datePublished) $datePublished = $issue->getDatePublished();
-        if ($datePublished) $datePublished = strtotime($datePublished);
+        if ($datePublished) {
+            $datePublished = strtotime($datePublished);
+        } else {
+            if ($issue) {
+                $datePublished = $issue->getDatePublished();
+            }
+        }
 
         // Include pub dates
-        if ($submission->getDatePublished()){
+        if ($datePublished) {
             $pubDateElement = $articleMetaElement->appendChild($this->createElement('pub-date'))
                 ->setAttribute('date-type', 'pub')->parentNode
                 ->setAttribute('publication-format','epub')->parentNode;
@@ -237,9 +250,9 @@ function createArticleMeta(Submission $submission, Journal $journal, Section $se
             $pageCount = $matchedPageTo - $matchedPageFrom + 1;
         }
 
-        $copyrightYear = $submission->getCopyrightYear();
-        $copyrightHolder = $submission->getLocalizedCopyrightHolder();
-        $licenseUrl = $submission->getLicenseURL();
+        $copyrightYear = $publication->getData('copyrightYear');
+        $copyrightHolder = $publication->getLocalizedData('copyrightHolder');
+        $licenseUrl = $publication->getData('licenseUrl');
         $ccBadge = Application::get()->getCCLicenseBadge($licenseUrl, $submission->getLocale())=== null?'':Application::get()->getCCLicenseBadge($licenseUrl, $submission->getLocale());
         if ($copyrightYear || $copyrightHolder || $licenseUrl || $ccBadge) {
             $permissionsElement = $articleMetaElement->appendChild($this->createElement('permissions'));
@@ -264,10 +277,15 @@ function createArticleMeta(Submission $submission, Journal $journal, Section $se
                 }
             }
         }
+
+        $router = $request->getRouter();
+        $dispatcher = $router->getDispatcher();
+
+        $url = $dispatcher->url($request, PKPApplication::ROUTE_PAGE, $journal->getPath(), 'article', 'view', $submission->getBestId(), null, null, true);
 
         $articleMetaElement
             ->appendChild($this->createElement('self-uri'))
-            ->setAttribute('xlink:href', $request->url($journal->getPath(), 'article', 'view', $submission->getBestArticleId()));
+            ->setAttribute('xlink:href', $url);
 
         $submissionKeywordDao = DAORegistry::getDAO('SubmissionKeywordDAO');
         foreach ($submissionKeywordDao->getKeywords($publication->getId(), $journal->getSupportedLocales()) as $locale => $keywords) {

diff --git a/tests/functional/ArticleTest.php b/tests/functional/ArticleTest.php
@@ -208,10 +208,10 @@ private function createOAIRecordMockObject(): OAIRecord
     public function testConvertToXml()
     {
         $record = $this->createOAIRecordMockObject();
-        $article = new Article($record);
-        $xml = $article->convertToXml($record);
+        $article = new Article();
+        $article->convertOAIToXml($record);
         self::assertXmlStringEqualsXmlFile($this->xmlFilePath.'ie1.xml', $article->saveXml());
-        self::assertTrue($xml);
+        self::assertTrue($article);
     }
 
     /**
@@ -221,8 +221,9 @@ public function testMapHtmlTagsForTitle(){
         $expected = '<bold>test</bold>';
         $htmlString = '<b>test</b>';
         $record = $this->createOAIRecordMockObject();
-        $article = new Article($record);
+        $article = new Article();
+        $article->convertOAIToXml($record);
         $actual = $article->mapHtmlTagsForTitle($htmlString);
-        self::assertEquals($expected,$actual);
+        self::assertEquals($expected, $actual);
     }
 }