PubMedExportDom::generateArticleDom PHP Method

    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', $journal->getLocalizedName());
        // check various ISSN fields to create the ISSN tag
        if ($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', $ISSN);
        }
        if ($issue->getShowVolume()) {
            XMLCustomWriter::createChildWithText($doc, $journalNode, 'Volume', $issue->getVolume());
        }
        if ($issue->getShowNumber()) {
            XMLCustomWriter::createChildWithText($doc, $journalNode, 'Issue', $issue->getNumber(), false);
        }
        $datePublished = $article->getDatePublished();
        if (!$datePublished) {
            $datePublished = $issue->getDatePublished();
        }
        if ($datePublished) {
            $pubDateNode =& PubMedExportDom::generatePubDateDom($doc, $datePublished, 'epublish');
            XMLCustomWriter::appendChild($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', $article->getLocalizedTitle());
        } else {
            XMLCustomWriter::createChildWithText($doc, $root, 'VernacularTitle', $article->getLocalizedTitle());
        }
        /* --- 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]+)\\s*-\\s*(e[0-9]+)/i", $pages, $matches)) {
            // e9 - e14, treated as page ranges
            XMLCustomWriter::createChildWithText($doc, $root, 'FirstPage', $matches[1]);
            XMLCustomWriter::createChildWithText($doc, $root, 'LastPage', $matches[2]);
        } elseif (preg_match("/(e[0-9]+)/i", $pages, $matches)) {
            // single elocation-id (eg. "e12")
            XMLCustomWriter::createChildWithText($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', $article->getBestArticleId());
            XMLCustomWriter::createChildWithText($doc, $root, 'LastPage', $article->getBestArticleId());
        }
        /* --- DOI --- */
        if ($doi = $article->getStoredPubId('doi')) {
            $doiNode =& XMLCustomWriter::createChildWithText($doc, $root, 'ELocationID', $doi, false);
            XMLCustomWriter::setAttribute($doiNode, 'EIdType', 'doi');
        }
        /* --- Language --- */
        XMLCustomWriter::createChildWithText($doc, $root, 'Language', strtoupper($article->getLanguage()), false);
        /* --- AuthorList --- */
        $authorListNode =& XMLCustomWriter::createElement($doc, 'AuthorList');
        XMLCustomWriter::appendChild($root, $authorListNode);
        $authorIndex = 0;
        foreach ($article->getAuthors() as $author) {
            $authorNode =& PubMedExportDom::generateAuthorDom($doc, $author, $authorIndex++);
            XMLCustomWriter::appendChild($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->getStoredPubId('publisher-id')) {
            $articleIdListNode =& XMLCustomWriter::createElement($doc, 'ArticleIdList');
            XMLCustomWriter::appendChild($root, $articleIdListNode);
            $articleIdNode =& XMLCustomWriter::createChildWithText($doc, $articleIdListNode, 'ArticleId', $article->getStoredPubId('publisher-id'));
            XMLCustomWriter::setAttribute($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->getId());
        // 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)) {
            $submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO');
            $submissionFile = $submissionFileDao->getLatestRevision($revisedFileId);
            if ($submissionFile) {
                $revisedNode =& PubMedExportDom::generatePubDateDom($doc, $submissionFile->getDateModified(), 'revised');
                XMLCustomWriter::appendChild($historyNode, $revisedNode);
            }
        }
        /* --- Abstract --- */
        if ($article->getLocalizedAbstract()) {
            $abstractNode = XMLCustomWriter::createChildWithText($doc, $root, 'Abstract', strip_tags($article->getLocalizedAbstract()), false);
        }
        return $root;
    }

 function exportIssues(&$journal, &$issues, $outputFile = null)
 {
     $this->import('PubMedExportDom');
     $doc =& PubMedExportDom::generatePubMedDom();
     $articleSetNode =& PubMedExportDom::generateArticleSetDom($doc);
     $sectionDao = DAORegistry::getDAO('SectionDAO');
     $publishedArticleDao = DAORegistry::getDAO('PublishedArticleDAO');
     foreach ($issues as $issue) {
         foreach ($sectionDao->getByIssueId($issue->getId()) as $section) {
             foreach ($publishedArticleDao->getPublishedArticlesBySectionId($section->getId(), $issue->getId()) as $article) {
                 $articleNode = PubMedExportDom::generateArticleDom($doc, $journal, $issue, $section, $article);
                 XMLCustomWriter::appendChild($articleSetNode, $articleNode);
             }
         }
     }
     if (!empty($outputFile)) {
         if (($h = fopen($outputFile, 'w')) === false) {
             return false;
         }
         fwrite($h, XMLCustomWriter::getXML($doc));
         fclose($h);
     } else {
         header("Content-Type: application/xml");
         header("Cache-Control: private");
         header("Content-Disposition: attachment; filename=\"pubmed.xml\"");
         XMLCustomWriter::printXML($doc);
     }
     return true;
 }