plugins/importexport/pubmed/PubMedExportDom.inc.php

<?php

// $Id: PubMedExportDom.inc.php,v 1.18 2008/07/01 01:16:14 asmecher Exp $


import('xml.XMLCustomWriter');

define('PUBMED_DTD_URL', 'http://www.ncbi.nlm.nih.gov:80/entrez/query/static/PubMed.dtd');
define('PUBMED_DTD_ID', '-//NLM//DTD PubMed 2.0//EN');

class PubMedExportDom {

   function &generatePubMedDom() {
      // create the output XML document in DOM with a root node
      $doc = &XMLCustomWriter::createDocument('ArticleSet', PUBMED_DTD_ID, PUBMED_DTD_URL);

      return $doc;
   }

   function &generateArticleSetDom(&$doc) {
      $root = &XMLCustomWriter::createElement($doc, 'ArticleSet');
      XMLCustomWriter::appendChild($doc, $root);

      return $root;
   }

   function &generateArticleDom(&$doc, &$journal, &$issue, &$section, &$article) {

      // register the editor submission DAO for use later
      $editorSubmissionDao = &DAORegistry::getDAO('EditorSubmissionDAO');

      /* --- Article --- */
      $root = &XMLCustomWriter::createElement($doc, 'Article');

      /* --- Journal --- */
      $journalNode = &XMLCustomWriter::createElement($doc, 'Journal');
      XMLCustomWriter::appendChild($root, $journalNode);

      $publisherInstitution = $journal->getSetting('publisherInstitution');
      $publisherNode = XMLCustomWriter::createChildWithText($doc, $journalNode, 'PublisherName', $publisherInstitution);

      XMLCustomWriter::createChildWithText($doc, $journalNode, 'JournalTitle', $journal->getJournalTitle());

      // check various ISSN fields to create the ISSN tag
      if ($journal->getSetting('printIssn') != '') $ISSN = $journal->getSetting('printIssn');
      elseif ($journal->getSetting('issn') != '') $ISSN = $journal->getSetting('issn');
      elseif ($journal->getSetting('onlineIssn') != '') $ISSN = $journal->getSetting('onlineIssn');
      else $ISSN = '';

      if ($ISSN != '') XMLCustomWriter::createChildWithText($doc, $journalNode, 'Issn', $ISSN);

      XMLCustomWriter::createChildWithText($doc, $journalNode, 'Volume', $issue->getVolume());
      XMLCustomWriter::createChildWithText($doc, $journalNode, 'Issue', $issue->getNumber(), false);

      $pubDateNode =& PubMedExportDom::generatePubDateDom($doc, $article->getDatePublished(), 'epublish');
      XMLCustomWriter::appendChild($journalNode, $pubDateNode);

      /* --- Replaces --- */
      // this creates a blank replaces tag since OJS doesn't contain PMID metadata
//    XMLCustomWriter::createChildWithText($doc, $root, 'Replaces', '');

      /* --- ArticleTitle / VernacularTitle --- */
      // there is some ambiguity between whether to use 
      // article->getlanguage or journal->getlocale
      // PubMed requires english titles for ArticleTitle
      $language = $article->getLanguage();
      if ($language == 'en' || $language == '' ) {
         XMLCustomWriter::createChildWithText($doc, $root, 'ArticleTitle', $article->getArticleTitle());
      } else {
         XMLCustomWriter::createChildWithText($doc, $root, 'VernacularTitle', $article->getArticleTitle());
      }

      /* --- FirstPage / LastPage --- */
      // there is some ambiguity for online journals as to what
      // "page numbers" are; for example, some journals (eg. JMIR)
      // use the "e-location ID" as the "page numbers" in PubMed
      $pages = $article->getPages();
      if (preg_match("/([0-9]+)\s*-\s*([0-9]+)/i", $pages, $matches)) {
         // simple pagination (eg. "pp. 3-      8")
         XMLCustomWriter::createChildWithText($doc, $root, 'FirstPage', $matches[1]);        
         XMLCustomWriter::createChildWithText($doc, $root, 'LastPage', $matches[2]);
      }elseif (preg_match("/(e[0-9]+)/i", $pages, $matches)) {
         // elocation-id (eg. "e12")
         XMLCustomWriter::createChildWithText($doc, $root, 'FirstPage', $matches[1]);
         XMLCustomWriter::createChildWithText($doc, $root, 'LastPage', $matches[1]);   
      } else {
         // we need to insert something, so use the best ID possible
         XMLCustomWriter::createChildWithText($doc, $root, 'FirstPage', $article->getBestArticleId($journal));       
         XMLCustomWriter::createChildWithText($doc, $root, 'LastPage', $article->getBestArticleId($journal));        
      }

      /* --- Language --- */
      XMLCustomWriter::createChildWithText($doc, $root, 'Language', strtoupper($article->getLanguage()), false);

      /* --- AuthorList --- */
      $authorListNode = &XMLCustomWriter::createElement($doc, 'AuthorList');
      XMLCustomWriter::appendChild($root, $authorListNode);

      foreach ($article->getAuthors() as $author) {
         $authorNode =& PubMedExportDom::generateAuthorDom($doc, $author);
         XMLCustomWriter::appendChild($authorListNode, $authorNode);
      }

      /* --- ArticleIdList --- */
      // Pubmed will accept two types of article identifier: pii and doi
      // how this is handled is journal-specific, and will require either
      // configuration in the plugin, or an update to the core code.
      // this is also related to DOI-handling within OJS
      if ($article->getPublicArticleId()) {
         $articleIdListNode = &XMLCustomWriter::createElement($doc, 'ArticleIdList');
         XMLCustomWriter::appendChild($root, $articleIdListNode);

         $articleIdNode = &XMLCustomWriter::createChildWithText($doc, $articleIdListNode, 'ArticleId', $article->getPublicArticleId());
         XMLCustomWriter::setAttribute($articleIdNode, 'IdType', 'pii');
      }

      /* --- History --- */
      $historyNode = &XMLCustomWriter::createElement($doc, 'History');
      XMLCustomWriter::appendChild($root, $historyNode);

      // date manuscript received for review
      $receivedNode =& PubMedExportDom::generatePubDateDom($doc, $article->getDateSubmitted(), 'received');
      XMLCustomWriter::appendChild($historyNode, $receivedNode);

      // accepted for publication
      $editordecisions = $editorSubmissionDao->getEditorDecisions($article->getArticleId());

      // if there are multiple decisions, make sure we get the accepted date
      $editordecision = array_pop($editordecisions);
      while ($editordecision['decision'] != SUBMISSION_EDITOR_DECISION_ACCEPT && count($editordecisions) > 0) $editordecision = array_pop($editordecisions);

      if ($editordecision != '') {
         $acceptedNode =& PubMedExportDom::generatePubDateDom($doc, $editordecision['dateDecided'], 'accepted');
         XMLCustomWriter::appendChild($historyNode, $acceptedNode);
      }

      // article revised by publisher or author
      // check if there is a revised version; if so, generate a revised tag
      $revisedFileID = $article->getRevisedFileId();
      if (!empty($revisedFileID)) {
         $articleFileDao = &DAORegistry::getDAO('ArticleFileDAO');
         $articleFile = &$articleFileDao->getArticleFile($revisedFileID);

         $revisedNode =& PubMedExportDom::generatePubDateDom($doc, $articleFile->getDateModified(), 'revised');
         XMLCustomWriter::appendChild($historyNode, $revisedNode);
      }

      /* --- Abstract --- */
      if ($article->getArticleAbstract()) {
         $abstractNode = XMLCustomWriter::createChildWithText($doc, $root, 'Abstract', strip_tags($article->getArticleAbstract()), false);
      }

      return $root;
   }

   function &generateAuthorDom(&$doc, &$author) {
      $root = &XMLCustomWriter::createElement($doc, 'Author');

      XMLCustomWriter::createChildWithText($doc, $root, 'FirstName', ucfirst($author->getFirstName()));
      XMLCustomWriter::createChildWithText($doc, $root, 'MiddleName', ucfirst($author->getMiddleName()), false);
      XMLCustomWriter::createChildWithText($doc, $root, 'LastName', ucfirst($author->getLastName()));

      if ($author->getPrimaryContact()) {
         XMLCustomWriter::createChildWithText($doc, $root, 'Affiliation', $author->getAffiliation() . '. ' . $author->getEmail(), false);
      }

      return $root;
   }

   function &generatePubDateDom(&$doc, $pubdate, $pubstatus) {
      $root = &XMLCustomWriter::createElement($doc, 'PubDate');

      XMLCustomWriter::setAttribute($root, 'PubStatus', $pubstatus);

      XMLCustomWriter::createChildWithText($doc, $root, 'Year', date('Y', strtotime($pubdate)) );
      XMLCustomWriter::createChildWithText($doc, $root, 'Month', date('m', strtotime($pubdate)), false );
      XMLCustomWriter::createChildWithText($doc, $root, 'Day', date('d', strtotime($pubdate)), false );

      return $root;
   }

}

?>

---