PreprintCrossrefXmlFilter.inc.php

<?php
 
import('lib.pkp.plugins.importexport.native.filter.NativeExportFilter');
 
class PreprintCrossrefXmlFilter extends NativeExportFilter {
   function __construct($filterGroup) {
      $this->setDisplayName('Crossref XML preprint export');
      parent::__construct($filterGroup);
   }
 
   //
   // Implement template methods from PersistableFilter
   //
   function getClassName() {
      return 'plugins.importexport.crossref.filter.PreprintCrossrefXmlFilter';
   }
 
   //
   // Implement template methods from Filter
   //
   function &process(&$pubObjects) {
      // Create the XML document
      $doc = new DOMDocument('1.0', 'utf-8');
      $doc->preserveWhiteSpace = false;
      $doc->formatOutput = true;
      $deployment = $this->getDeployment();
      $context = $deployment->getContext();
 
      // Create the root node
      $rootNode = $this->createRootNode($doc);
      $doc->appendChild($rootNode);
 
      // Create and appet the 'head' node and all parts inside it
      $rootNode->appendChild($this->createHeadNode($doc));
 
      // Create and append the 'body' node, that contains everything
      $bodyNode = $doc->createElementNS($deployment->getNamespace(), 'body');
      $rootNode->appendChild($bodyNode);
 
      foreach($pubObjects as $pubObject) {
         $publications = $pubObject->getData('publications');
         // Use array reverse so that the latest version of the submission is first in the xml output and the DOI relations do not cause an error with Crossref
         $publications = array_reverse($publications, true);
         foreach ($publications as $publication) {
            if ($publication->getStoredPubId('doi')) {               
               $postedContentNode = $this->createPostedContentNode($doc, $publication, $pubObject);
               $bodyNode->appendChild($postedContentNode);
            }
         }
      }
      return $doc;
   }
 
   //
   // Submission conversion functions
   //
 
   function createRootNode($doc) {
      $deployment = $this->getDeployment();
      $rootNode = $doc->createElementNS($deployment->getNamespace(), $deployment->getRootElementName());
      $rootNode->setAttributeNS('http://www.w3.org/2000/xmlns/', 'xmlns:xsi', $deployment->getXmlSchemaInstance());
      $rootNode->setAttributeNS('http://www.w3.org/2000/xmlns/', 'xmlns:jats', $deployment->getJATSNamespace());
      $rootNode->setAttributeNS('http://www.w3.org/2000/xmlns/', 'xmlns:ai', $deployment->getAINamespace());
      $rootNode->setAttributeNS('http://www.w3.org/2000/xmlns/', 'xmlns:rel', $deployment->getRELNamespace());
      $rootNode->setAttribute('version', $deployment->getXmlSchemaVersion());
      $rootNode->setAttribute('xsi:schemaLocation', $deployment->getNamespace() . ' ' . $deployment->getSchemaFilename());
      return $rootNode;
   }
 
   function createHeadNode($doc) {
      $deployment = $this->getDeployment();
      $context = $deployment->getContext();
      $plugin = $deployment->getPlugin();
      $headNode = $doc->createElementNS($deployment->getNamespace(), 'head');
      $headNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'doi_batch_id', htmlspecialchars($context->getData('initials', $context->getPrimaryLocale()) . '_' . time(), ENT_COMPAT, 'UTF-8')));
      $headNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'timestamp', time()));
      $depositorNode = $doc->createElementNS($deployment->getNamespace(), 'depositor');
      $depositorName = $plugin->getSetting($context->getId(), 'depositorName');
      if (empty($depositorName)) {
         $depositorName = $context->getData('supportName');
      }
      $depositorEmail = $plugin->getSetting($context->getId(), 'depositorEmail');
      if (empty($depositorEmail)) {
         $depositorEmail = $context->getData('supportEmail');
      }
      $depositorNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'depositor_name', htmlspecialchars($depositorName, ENT_COMPAT, 'UTF-8')));
      $depositorNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'email_address', htmlspecialchars($depositorEmail, ENT_COMPAT, 'UTF-8')));
      $headNode->appendChild($depositorNode);
      $publisherServer = $context->getLocalizedName();
      $headNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'registrant', htmlspecialchars($publisherServer, ENT_COMPAT, 'UTF-8')));
      return $headNode;
   }
 
   function createPostedContentNode($doc, $publication, $submission) {
      assert(is_a($publication, 'Publication'));
      $deployment = $this->getDeployment();
      $context = $deployment->getContext();
      $request = Application::get()->getRequest();
 
      $locale = $publication->getData('locale');
 
      $postedContentNode = $doc->createElementNS($deployment->getNamespace(), 'posted_content');
      $postedContentNode->setAttribute('type', 'preprint');
 
      // contributors
      $contributorsNode = $doc->createElementNS($deployment->getNamespace(), 'contributors');
      $authors = $publication->getData('authors');
      $isFirst = true;
      foreach ($authors as $author) {
         $personNameNode = $doc->createElementNS($deployment->getNamespace(), 'person_name');
         $personNameNode->setAttribute('contributor_role', 'author');
         if ($isFirst) {
            $personNameNode->setAttribute('sequence', 'first');
         } else {
            $personNameNode->setAttribute('sequence', 'additional');
         }
         
         $familyNames = $author->getFamilyName(null);
         $givenNames = $author->getGivenName(null);
 
         // Check if both givenName and familyName is set for the submission language.
         if (isset($familyNames[$locale]) && isset($givenNames[$locale])) {
            $personNameNode->setAttribute('language', PKPLocale::getIso1FromLocale($locale));
            $personNameNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'given_name', htmlspecialchars(ucfirst($givenNames[$locale]), ENT_COMPAT, 'UTF-8')));
            $personNameNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'surname', htmlspecialchars(ucfirst($familyNames[$locale]), ENT_COMPAT, 'UTF-8')));
 
            $hasAltName = false;
            foreach($familyNames as $otherLocal => $familyName) {
               if ($otherLocal != $locale && isset($familyName) && !empty($familyName)) {
                  if (!$hasAltName) {
                     $altNameNode = $doc->createElementNS($deployment->getNamespace(), 'alt-name');
                     $personNameNode->appendChild($altNameNode);
 
                     $hasAltName = true;
                  }
 
                  $nameNode = $doc->createElementNS($deployment->getNamespace(), 'name');
                  $nameNode->setAttribute('language', PKPLocale::getIso1FromLocale($otherLocal));
 
                  $nameNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'surname', htmlspecialchars(ucfirst($familyName), ENT_COMPAT, 'UTF-8')));
                  if (isset($givenNames[$otherLocal]) && !empty($givenNames[$otherLocal])) {
                     $nameNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'given_name', htmlspecialchars(ucfirst($givenNames[$otherLocal]), ENT_COMPAT, 'UTF-8')));
                  }
 
                  $altNameNode->appendChild($nameNode);
               }
            }
 
         } else {
            $personNameNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'surname', htmlspecialchars(ucfirst($author->getFullName(false)), ENT_COMPAT, 'UTF-8')));
         }
 
         if ($author->getData('orcid')) {
            $personNameNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'ORCID', $author->getData('orcid')));
         }
         $contributorsNode->appendChild($personNameNode);
         $isFirst = false;
      }
      $postedContentNode->appendChild($contributorsNode);
 
      // Titles
      $titlesNode = $doc->createElementNS($deployment->getNamespace(), 'titles');
      $titlesNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'title', htmlspecialchars($publication->getData('title', $submission->getLocale()), ENT_COMPAT, 'UTF-8')));
      if ($subtitle = $publication->getData('subtitle', $submission->getLocale())) $titlesNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'subtitle', htmlspecialchars($subtitle, ENT_COMPAT, 'UTF-8')));
      $postedContentNode->appendChild($titlesNode);
 
      // Posted date
      $postedContentNode->appendChild($this->createPostedDateNode($doc, $publication->getData('datePublished')));
 
      // license
      if ($publication->getData('licenseUrl')) {
         $licenseNode = $doc->createElementNS($deployment->getAINamespace(), 'ai:program');
         $licenseNode->setAttribute('name', 'AccessIndicators');
         $licenseNode->appendChild($node = $doc->createElementNS($deployment->getAINamespace(), 'ai:license_ref', htmlspecialchars($publication->getData('licenseUrl'), ENT_COMPAT, 'UTF-8')));
         $postedContentNode->appendChild($licenseNode);
      }
 
      // DOI relations
      if ($submission->getLatestPublication()->getStoredPubId('doi') && $submission->getLatestPublication()->getStoredPubId('doi') != $publication->getStoredPubId('doi')){
         $postedContentNode->appendChild($this->createRelationsDataNode($doc, $submission->getLatestPublication()->getStoredPubId('doi')));
      }
 
      // DOI data
      $postedContentNode->appendChild($this->createDOIDataNode($doc, $publication->getStoredPubId('doi'), $request->getDispatcher()->url($request, ROUTE_PAGE, null, 'preprint', 'view', [$submission->getBestId(), 'version', $publication->getId()], null, null, true)));
 
      return $postedContentNode;
   }
 
   function createPostedDateNode($doc, $objectPostedDate) {
      $deployment = $this->getDeployment();
      $postedDate = strtotime($objectPostedDate);
      $postedDateNode = $doc->createElementNS($deployment->getNamespace(), 'posted_date');
      if (date('m', $postedDate)) {
         $postedDateNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'month', date('m', $postedDate)));
      }
      if (date('d', $postedDate)) {
         $postedDateNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'day', date('d', $postedDate)));
      }
      $postedDateNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'year', date('Y', $postedDate)));
      return $postedDateNode;
   }
 
   function createDOIDataNode($doc, $doi, $url) {
      $deployment = $this->getDeployment();
      $doiDataNode = $doc->createElementNS($deployment->getNamespace(), 'doi_data');
      $doiDataNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'doi', htmlspecialchars($doi, ENT_COMPAT, 'UTF-8')));
      $doiDataNode->appendChild($node = $doc->createElementNS($deployment->getNamespace(), 'resource', htmlspecialchars($url, ENT_COMPAT, 'UTF-8')));
      return $doiDataNode;
   }
 
   function createRelationsDataNode($doc, $parentDoi) {
      $deployment = $this->getDeployment();
      $relationsDataNode = $doc->createElementNS($deployment->getRELNamespace(), 'rel:program');
      $relationsDataNode->setAttribute('name', 'relations');
 
      $relatedItemNode = $doc->createElementNS($deployment->getRELNamespace(), 'rel:related_item');
      $intraWorkRelationNode = $doc->createElementNS($deployment->getRELNamespace(), 'rel:intra_work_relation',  htmlspecialchars($parentDoi, ENT_COMPAT, 'UTF-8'));
      $intraWorkRelationNode->setAttribute('relationship-type', 'isVersionOf');
      $intraWorkRelationNode->setAttribute('identifier-type', 'doi');
      $relatedItemNode->appendChild($intraWorkRelationNode);
      $relationsDataNode->appendChild($relatedItemNode);
 
      return $relationsDataNode;
   }
}