ArticlePubMedXmlFilter.inc.php

<?php
 
import('lib.pkp.classes.filter.PersistableFilter');
 
class ArticlePubMedXmlFilter extends PersistableFilter {
   function __construct($filterGroup) {
      parent::__construct($filterGroup);
   }
 
 
   //
   // Implement template methods from PersistableFilter
   //
   function getClassName() {
      return 'plugins.importexport.pubmed.filter.ArticlePubMedXmlFilter';
   }
 
 
   //
   // Implement abstract methods from SubmissionPubMedXmlFilter
   //
   function getRepresentationExportFilterGroupName() {
      return 'article-galley=>pubmed-xml';
   }
 
   //
   // Implement template methods from Filter
   //
   function &process(&$submissions) {
      // Create the XML document
      $implementation = new DOMImplementation();
      $dtd = $implementation->createDocumentType('ArticleSet', '-//NLM//DTD PubMed 2.0//EN', 'http://www.ncbi.nlm.nih.gov/entrez/query/static/PubMed.dtd');
      $doc = $implementation->createDocument('', '', $dtd);
      $doc->preserveWhiteSpace = false;
      $doc->formatOutput = true;
 
      $issueDao = DAORegistry::getDAO('IssueDAO'); /* @var $issueDao IssueDAO */
      $journalDao = DAORegistry::getDAO('JournalDAO'); /* @var $journalDao JournalDAO */
      $journal = null;
 
      $rootNode = $doc->createElement('ArticleSet');
      foreach ($submissions as $submission) {
         // Fetch associated objects
         if (!$journal || $journal->getId() != $submission->getContextId()) {
            $journal = $journalDao->getById($submission->getContextId());
         }
         $issue = $issueDao->getBySubmissionId($submission->getId(), $journal->getId());
 
         $articleNode = $doc->createElement('Article');
         $articleNode->appendChild($this->createJournalNode($doc, $journal, $issue, $submission));
 
         $publication = $submission->getCurrentPublication();
 
         $locale = $publication->getData('locale');
         if ($locale == 'en_US') {
            $articleNode->appendChild($doc->createElement('ArticleTitle'))->appendChild($doc->createTextNode($publication->getLocalizedTitle($locale)));
         } else {
            $articleNode->appendChild($doc->createElement('VernacularTitle'))->appendChild($doc->createTextNode($publication->getLocalizedTitle($locale)));
         }
 
         $startPage = $publication->getStartingPage();
         $endPage = $publication->getEndingPage();
         if (isset($startPage) && $startPage !== '') {
            // We have a page range or e-location id
            $articleNode->appendChild($doc->createElement('FirstPage'))->appendChild($doc->createTextNode($startPage));
            $articleNode->appendChild($doc->createElement('LastPage'))->appendChild($doc->createTextNode($endPage));
         }
 
         if ($doi = $publication->getStoredPubId('doi')) {
            $doiNode = $doc->createElement('ELocationID');
            $doiNode->appendChild($doc->createTextNode($doi));
            $doiNode->setAttribute('EIdType', 'doi');
            $articleNode->appendChild($doiNode);
         }
 
         $articleNode->appendChild($doc->createElement('Language'))->appendChild($doc->createTextNode(AppLocale::get3LetterFrom2LetterIsoLanguage(substr($locale, 0, 2))));
 
         $authorListNode = $doc->createElement('AuthorList');
         foreach ((array) $publication->getData('authors') as $author) {
            $authorListNode->appendChild($this->generateAuthorNode($doc, $journal, $issue, $submission, $author));
         }
         $articleNode->appendChild($authorListNode);
 
         if ($publication->getStoredPubId('publisher-id')) {
            $articleIdListNode = $doc->createElement('ArticleIdList');
            $articleIdNode = $doc->createElement('ArticleId');
            $articleIdNode->appendChild($doc->createTextNode($publication->getStoredPubId('publisher-id')));
            $articleIdNode->setAttribute('IdType', 'pii');
            $articleIdListNode->appendChild($articleIdNode);
            $articleNode->appendChild($articleIdListNode);
         }
 
         // History
         $historyNode = $doc->createElement('History');
         $historyNode->appendChild($this->generatePubDateDom($doc, $submission->getDateSubmitted(), 'received'));
 
         $editDecisionDao = DAORegistry::getDAO('EditDecisionDAO'); /* @var $editDecisionDao EditDecisionDAO */
         $editDecisions = (array) $editDecisionDao->getEditorDecisions($submission->getId());
         do {
            $editorDecision = array_pop($editDecisions);
         } while ($editorDecision && $editorDecision['decision'] != SUBMISSION_EDITOR_DECISION_ACCEPT);
 
         if ($editorDecision) {
            $historyNode->appendChild($this->generatePubDateDom($doc, $editorDecision['dateDecided'], 'accepted'));
         }
         $articleNode->appendChild($historyNode);
 
         // FIXME: Revision dates
 
         if ($abstract = PKPString::html2text($publication->getLocalizedData('abstract', $locale))) {
            $articleNode->appendChild($doc->createElement('Abstract'))->appendChild($doc->createTextNode($abstract));
         }
 
         $rootNode->appendChild($articleNode);
      }
      $doc->appendChild($rootNode);
      return $doc;
   }
 
   function createJournalNode($doc, $journal, $issue, $submission) {
      $journalNode = $doc->createElement('Journal');
 
      $publisherNameNode = $doc->createElement('PublisherName');
      $publisherNameNode->appendChild($doc->createTextNode($journal->getData('publisherInstitution')));
      $journalNode->appendChild($publisherNameNode);
 
      $journalTitleNode = $doc->createElement('JournalTitle');
      $journalTitleNode->appendChild($doc->createTextNode($journal->getName($journal->getPrimaryLocale())));
      $journalNode->appendChild($journalTitleNode);
 
      // check various ISSN fields to create the ISSN tag
      if ($journal->getData('printIssn') != '') $issn = $journal->getData('printIssn');
      elseif ($journal->getData('issn') != '') $issn = $journal->getData('issn');
      elseif ($journal->getData('onlineIssn') != '') $issn = $journal->getData('onlineIssn');
      else $issn = '';
      if ($issn != '') $journalNode->appendChild($doc->createElement('Issn', $issn));
 
      if ($issue && $issue->getShowVolume()) $journalNode->appendChild($doc->createElement('Volume'))->appendChild($doc->createTextNode($issue->getVolume()));
      if ($issue && $issue->getShowNumber()) $journalNode->appendChild($doc->createElement('Issue'))->appendChild($doc->createTextNode($issue->getNumber()));
 
      $datePublished = null;
      if ($submission) $datePublished = $submission->getCurrentPublication()->getData('datePublished');
      if (!$datePublished && $issue) $datePublished = $issue->getDatePublished();
      if ($datePublished) {
         $journalNode->appendChild($this->generatePubDateDom($doc, $datePublished, 'epublish'));
      }
 
      return $journalNode;
   }
 
   function generateAuthorNode($doc, $journal, $issue, $submission, $author) {
      $authorElement = $doc->createElement('Author');
 
      if (empty($author->getLocalizedFamilyName())) {
         $authorElement->appendChild($node = $doc->createElement('FirstName'));
         $node->setAttribute('EmptyYN', 'Y');
         $authorElement->appendChild($doc->createElement('LastName'))->appendChild($doc->createTextNode(ucfirst($author->getLocalizedGivenName())));
      } else {
         $authorElement->appendChild($doc->createElement('FirstName'))->appendChild($doc->createTextNode(ucfirst($author->getLocalizedGivenName())));
         $authorElement->appendChild($doc->createElement('LastName'))->appendChild($doc->createTextNode(ucfirst($author->getLocalizedFamilyName())));
      }
      $authorElement->appendChild($doc->createElement('Affiliation'))->appendChild($doc->createTextNode($author->getLocalizedAffiliation() . '. ' . $author->getEmail()));
 
      return $authorElement;
   }
 
   function generatePubDateDom($doc, $pubDate, $pubStatus) {
      $pubDateNode = $doc->createElement('PubDate');
      $pubDateNode->setAttribute('PubStatus', $pubStatus);
 
      $pubDateNode->appendChild($doc->createElement('Year', date('Y', strtotime($pubDate))));
      $pubDateNode->appendChild($doc->createElement('Month', date('m', strtotime($pubDate))));
      $pubDateNode->appendChild($doc->createElement('Day', date('d', strtotime($pubDate))));
 
      return $pubDateNode;
   }
}