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<?php
/**
* @file plugins/importexport/crossref/classes/CrossRefExportDom.inc.php
*
* Copyright (c) 2013-2019 Simon Fraser University
* Copyright (c) 2003-2019 John Willinsky
* Distributed under the GNU GPL v2. For full terms see the file docs/COPYING.
*
* @class CrossRefExportDom
* @ingroup plugins_importexport_crossref_classes
*
* @brief CrossRef XML export format implementation.
*/
if (!class_exists('DOIExportDom')) { // Bug #7848
import('plugins.importexport.crossref.classes.DOIExportDom');
}
// XML attributes
define('CROSSREF_XMLNS_XSI' , 'http://www.w3.org/2001/XMLSchema-instance');
define('CROSSREF_XMLNS' , 'http://www.crossref.org/schema/4.3.6');
define('CROSSREF_VERSION' , '4.3.6');
define('CROSSREF_XSI_SCHEMAVERSION' , '4.3.6');
define('CROSSREF_XSI_SCHEMALOCATION' , 'http://www.crossref.org/schema/4.3.6 https://www.crossref.org/schemas/crossref4.3.6.xsd');
class CrossRefExportDom extends DOIExportDom {
//
// Constructor
//
/**
* Constructor
* @param $request Request
* @param $plugin DOIExportPlugin
* @param $journal Journal
* @param $objectCache PubObjectCache
*/
function CrossRefExportDom(&$request, &$plugin, &$journal, &$objectCache) {
// Configure the DOM.
parent::DOIExportDom($request, $plugin, $journal, $objectCache);
}
//
// Public methods
//
/**
* @see DOIExportDom::generate()
*/
function &generate(&$objects) {
$journal =& $this->getJournal();
// Create the XML document and its root element.
$doc =& $this->getDoc();
$rootElement =& $this->rootElement();
XMLCustomWriter::appendChild($doc, $rootElement);
// Create Head Node and all parts inside it
$head =& $this->_generateHeadDom($doc, $journal);
// attach it to the root node
XMLCustomWriter::appendChild($rootElement, $head);
// the body node contains everything
$bodyNode =& XMLCustomWriter::createElement($doc, 'body');
XMLCustomWriter::appendChild($rootElement, $bodyNode);
foreach($objects as $object) {
// Retrieve required publication objects.
$pubObjects =& $this->retrievePublicationObjects($object);
extract($pubObjects);
$issue =& $pubObjects['issue'];
if (is_a($object, 'Issue')) {
foreach ($pubObjects['articlesByIssue'] as $article) {
if ($article->getPubId('doi')) {
$this->_appendArticleXML($doc, $journal, $issue, $article, $bodyNode);
}
}
} else {
$article =& $pubObjects['article'];
if ($article->getPubId('doi')) {
$this->_appendArticleXML($doc, $journal, $issue, $article, $bodyNode);
}
}
}
return $doc;
}
//
// Implementation of template methods from DOIExportDom
//
/**
* @see DOIExportDom::getRootElementName()
*/
function getRootElementName() {
return 'doi_batch';
}
/**
* @see DOIExportDom::getNamespace()
*/
function getNamespace() {
return CROSSREF_XMLNS;
}
/**
* @see DOIExportDom::getXmlSchemaVersionn()
*/
function getXmlSchemaVersion() {
return CROSSREF_XSI_SCHEMAVERSION;
}
/**
* @see DOIExportDom::getXmlSchemaLocation()
*/
function getXmlSchemaLocation() {
return CROSSREF_XSI_SCHEMALOCATION;
}
/**
* @see DOIExportDom::retrievePublicationObjects()
*/
function &retrievePublicationObjects(&$object) {
// Initialize local variables.
$nullVar = null;
$journal =& $this->getJournal();
$cache =& $this->getCache();
// Retrieve basic OJS objects.
$publicationObjects = parent::retrievePublicationObjects($object);
// Retrieve additional related objects.
// For articles: no additional objects needed for CrossRef:
// galleys are not considered and
// supp files will be retrieved when crating the XML
// Note: article issue is already retrieved by the parent method
if (is_a($object, 'PublishedArticle')) {
$article =& $publicationObjects['article'];
}
// For issues: Retrieve all articles of the issue:
if (is_a($object, 'Issue')) {
// Articles by issue.
assert(isset($publicationObjects['issue']));
$issue =& $publicationObjects['issue'];
$publicationObjects['articlesByIssue'] =& $this->retrieveArticlesByIssue($issue);
}
return $publicationObjects;
}
//
// Private helper methods
//
/**
* Generate the <head> tag that accompanies each submission
* @param $doc XMLNode
* @param $journal Journal
* @return XMLNode
*/
function &_generateHeadDom(&$doc, &$journal) {
$head =& XMLCustomWriter::createElement($doc, 'head');
// DOI batch ID is a simple tracking ID: initials + timestamp
XMLCustomWriter::createChildWithText($doc, $head, 'doi_batch_id', $journal->getSetting('initials', $journal->getPrimaryLocale()) . '_' . time());
XMLCustomWriter::createChildWithText($doc, $head, 'timestamp', time());
$journalId = $journal->getId();
/* Depositor defaults to the Journal's technical Contact */
$plugin = $this->_plugin;
$depositorName = $plugin->getSetting($journalId, 'depositorName');
if (empty($depositorName)) {
$depositorName = $journal->getSetting('supportName');
}
$depositorEmail = $plugin->getSetting($journalId, 'depositorEmail');
if (empty($depositorEmail)) {
$depositorEmail = $journal->getSetting('supportEmail');
}
$depositorNode =& $this->_generateDepositorDom($doc, $depositorName, $depositorEmail);
XMLCustomWriter::appendChild($head, $depositorNode);
/* The registrant is assumed to be the Publishing institution */
$publisherInstitution = $journal->getSetting('publisherInstitution');
XMLCustomWriter::createChildWithText($doc, $head, 'registrant', $publisherInstitution);
return $head;
}
/**
* Generate depositor node
* @param $doc XMLNode
* @param $name string
* @param $email string
* @return XMLNode
*/
function &_generateDepositorDom(&$doc, $name, $email) {
$depositor =& XMLCustomWriter::createElement($doc, 'depositor');
XMLCustomWriter::createChildWithText($doc, $depositor, 'depositor_name', $name);
XMLCustomWriter::createChildWithText($doc, $depositor, 'email_address', $email);
return $depositor;
}
/**
* Generate and append the XML per article
* @param $doc XMLNode
* @param $journal Journal
* @param $issue Issue
* @param $article Article
* @param $bodyNode XMLNode
*/
function _appendArticleXML(&$doc, &$journal, &$issue, &$article, &$bodyNode) {
$sectionId = $article->getSectionId();
$sectionDao =& DAORegistry::getDAO('SectionDAO');
$section =& $sectionDao->getSection($sectionId);
// Create the journal node
$journalNode =& XMLCustomWriter::createElement($doc, 'journal');
$journalMetadataNode =& $this->_generateJournalMetadataDom($doc, $journal);
XMLCustomWriter::appendChild($journalNode, $journalMetadataNode);
// Create the journal_issue node
$journalIssueNode =& $this->_generateJournalIssueDom($doc, $journal, $issue, $section, $article);
XMLCustomWriter::appendChild($journalNode, $journalIssueNode);
// Create the article node
$journalArticleNode =& $this->_generateJournalArticleDom($doc, $journal, $issue, $section, $article);
XMLCustomWriter::appendChild($journalNode, $journalArticleNode);
XMLCustomWriter::appendChild($bodyNode, $journalNode);
}
/**
* Generate metadata for journal - accompanies every article
* @param $doc XMLNode
* @param $journal Journal
* @return XMLNode
*/
function &_generateJournalMetadataDom(&$doc, &$journal) {
$journalMetadataNode =& XMLCustomWriter::createElement($doc, 'journal_metadata');
/* Full Title of Journal */
$journalTitle = $journal->getTitle($journal->getPrimaryLocale());
// Attempt a fall back, in case the localized name is not set.
if ($journalTitle == '') {
$journalTitle = $journal->getSetting('abbreviation', $journal->getPrimaryLocale());
}
XMLCustomWriter::createChildWithText($doc, $journalMetadataNode, 'full_title', $journalTitle);
/* Abbreviated title - defaulting to initials if no abbreviation found */
if ($journal->getSetting('abbreviation', $journal->getPrimaryLocale()) != '' ) {
XMLCustomWriter::createChildWithText($doc, $journalMetadataNode, 'abbrev_title', $journal->getSetting('abbreviation', $journal->getPrimaryLocale()));
}
else {
XMLCustomWriter::createChildWithText($doc, $journalMetadataNode, 'abbrev_title', $journal->getSetting('initials', $journal->getPrimaryLocale()));
}
/* Both ISSNs are permitted for CrossRef, so sending whichever one (or both) */
if ( $ISSN = $journal->getSetting('onlineIssn') ) {
$onlineISSN =& XMLCustomWriter::createChildWithText($doc, $journalMetadataNode, 'issn', $ISSN);
XMLCustomWriter::setAttribute($onlineISSN, 'media_type', 'electronic');
}
/* Both ISSNs are permitted for CrossRef so sending whichever one (or both) */
if ( $ISSN = $journal->getSetting('printIssn') ) {
$printISSN =& XMLCustomWriter::createChildWithText($doc, $journalMetadataNode, 'issn', $ISSN);
XMLCustomWriter::setAttribute($printISSN, 'media_type', 'print');
}
return $journalMetadataNode;
}
/**
* Generate journal issue tag to accompany every article
* @param $doc XMLNode
* @param $journal Journal
* @param $issue Issue
* @param $section Section
* @param $article Article
* @return XMLNode
*/
function &_generateJournalIssueDom(&$doc, &$journal, &$issue, &$section, &$article) {
$journalIssueNode =& XMLCustomWriter::createElement($doc, 'journal_issue');
if ($issue->getDatePublished()) {
$publicationDateNode =& $this->_generatePublisherDateDom($doc, $issue->getDatePublished());
XMLCustomWriter::appendChild($journalIssueNode, $publicationDateNode);
}
if ($issue->getVolume()){
$journalVolumeNode =& XMLCustomWriter::createElement($doc, 'journal_volume');
XMLCustomWriter::appendChild($journalIssueNode, $journalVolumeNode);
XMLCustomWriter::createChildWithText($doc, $journalVolumeNode, 'volume', $issue->getVolume());
}
if ($issue->getNumber()) {
XMLCustomWriter::createChildWithText($doc, $journalIssueNode, 'issue', $issue->getNumber());
}
if ($issue->getDatePublished() && $issue->getPubId('doi')) {
$issueDoiNode =& $this->_generateDOIdataDom($doc, $issue->getPubId('doi'), Request::url($journal->getPath(), 'issue', 'view', $issue->getBestIssueId($journal)));
XMLCustomWriter::appendChild($journalIssueNode, $issueDoiNode);
}
return $journalIssueNode;
}
/**
* Generate the journal_article node (the heart of the file).
* @param $doc XMLNode
* @param $journal Journal
* @param $issue Issue
* @param $section Section
* @param $article Article
* @return XMLNode
*/
function &_generateJournalArticleDom(&$doc, &$journal, &$issue, &$section, &$article) {
// Create the base node
$journalArticleNode =& XMLCustomWriter::createElement($doc, 'journal_article');
XMLCustomWriter::setAttribute($journalArticleNode, 'publication_type', 'full_text');
XMLCustomWriter::setAttribute($journalArticleNode, 'metadata_distribution_opts', 'any');
/* Titles */
$titlesNode =& XMLCustomWriter::createElement($doc, 'titles');
XMLCustomWriter::createChildWithText($doc, $titlesNode, 'title', $article->getTitle($article->getLocale()));
XMLCustomWriter::appendChild($journalArticleNode, $titlesNode);
/* AuthorList */
$contributorsNode =& XMLCustomWriter::createElement($doc, 'contributors');
$isFirst = true;
foreach ($article->getAuthors() as $author) {
$authorNode =& $this->_generateAuthorDom($doc, $author, $isFirst);
$isFirst = false;
XMLCustomWriter::appendChild($contributorsNode, $authorNode);
}
XMLCustomWriter::appendChild($journalArticleNode, $contributorsNode);
/* Abstracts */
if ($article->getAbstract($journal->getPrimaryLocale())) {
$abstractNode =& XMLCustomWriter::createElement($doc, 'jats:abstract');
XMLCustomWriter::createChildWithText($doc, $abstractNode, 'jats:p', PKPString::html2utf(strip_tags($article->getAbstract($journal->getPrimaryLocale()))));
XMLCustomWriter::appendChild($journalArticleNode, $abstractNode);
}
/* publication date of article */
// if there is no article publication date, take the issue publication date
$datePublished = $article->getDatePublished() ? $article->getDatePublished() : $issue->getDatePublished();
if ($datePublished) {
$publicationDateNode =& $this->_generatePublisherDateDom($doc, $datePublished);
XMLCustomWriter::appendChild($journalArticleNode, $publicationDateNode);
}
/* publisher_item is the article pages */
// CrossRef requires first_page and last_page of any contiguous range, then any other ranges go in other_pages
$pages = $article->getPageArray();
if (!empty($pages)) {
$firstRange = array_shift($pages);
$firstPage = array_shift($firstRange);
if (count($firstRange)) {
// There is a first page and last page for the first range
$lastPage = array_shift($firstRange);
} else {
// There is not a range in the first segment
$lastPage = '';
}
// CrossRef accepts no punctuation in first_page or last_page
if ((!empty($firstPage) || $firstPage === "0") && !preg_match('/[^[:alnum:]]/', $firstPage) && !preg_match('/[^[:alnum:]]/', $lastPage)) {
$pageNode =& XMLCustomWriter::createElement($doc, 'pages');
XMLCustomWriter::createChildWithText($doc, $pageNode, 'first_page', $firstPage);
if ($lastPage != '') {
XMLCustomWriter::createChildWithText($doc, $pageNode, 'last_page', $lastPage);
}
$otherPages = '';
foreach ($pages as $range) {
$otherPages .= ($otherPages ? ',' : '').implode('-', $range);
}
if ($otherPages != '') {
XMLCustomWriter::createChildWithText($doc, $pageNode, 'other_pages', $otherPages);
}
XMLCustomWriter::appendChild($journalArticleNode, $pageNode);
}
}
/* License URL */
if ($article->getLicenseUrl()) {
$licenseNode =& XMLCustomWriter::createElement($doc, 'ai:program');
XMLCustomWriter::setAttribute($licenseNode, 'name', 'AccessIndicators');
XMLCustomWriter::createChildWithText($doc, $licenseNode, 'ai:license_ref', $article->getLicenseUrl());
XMLCustomWriter::appendChild($journalArticleNode, $licenseNode);
}
// DOI data node
$articleGalleyDao = DAORegistry::getDAO('ArticleGalleyDAO');
$DOIdataNode =& $this->_generateDOIdataDom($doc, $article->getPubId('doi'), Request::url($journal->getPath(), 'article', 'view', $article->getBestArticleId()), $articleGalleyDao->getGalleysByArticle($article->getId()));
XMLCustomWriter::appendChild($journalArticleNode, $DOIdataNode);
/* Component list (supplementary files) */
$componentListNode =& $this->_generateComponentListDom($doc, $journal, $article);
if ($componentListNode) {
XMLCustomWriter::appendChild($journalArticleNode, $componentListNode);
}
return $journalArticleNode;
}
/**
* Generate the component_list node (supplementary files).
* @param $doc XMLNode
* @param $journal Journal
* @param $issue Issue
* @param $section Section
* @param $article Article
* @return XMLNode
*/
function &_generateComponentListDom(&$doc, &$journal, &$article) {
$suppFiles =& $article->getSuppFiles();
$createComponentList = false;
foreach ($suppFiles as $suppFile) {
if ($suppFile->getPubId('doi')) {
$createComponentList = true;
break;
}
}
if ($createComponentList) {
// Create the base node
$componentListNode =& XMLCustomWriter::createElement($doc, 'component_list');
// Run through supp files and add component nodes.
foreach($suppFiles as $suppFile) {
if ($suppFile->getPubId('doi')) {
$componentNode =& XMLCustomWriter::createElement($doc, 'component');
XMLCustomWriter::setAttribute($componentNode, 'parent_relation', 'isPartOf');
/* Titles */
$suppFileTitle = $suppFile->getSuppFileTitle();
if (!empty($suppFileTitle)) {
$titlesNode =& XMLCustomWriter::createElement($doc, 'titles');
XMLCustomWriter::createChildWithText($doc, $titlesNode, 'title', $suppFileTitle);
XMLCustomWriter::appendChild($componentNode, $titlesNode);
}
// DOI data node
$suppFileUrl = Request::url(
$journal->getPath(), 'article', 'downloadSuppFile',
array($article->getId(), $suppFile->getBestSuppFileId($journal))
);
$suppFileDoiNode =& $this->_generateDOIdataDom($doc, $suppFile->getPubId('doi'), $suppFileUrl);
XMLCustomWriter::appendChild($componentNode, $suppFileDoiNode);
}
XMLCustomWriter::appendChild($componentListNode, $componentNode);
unset($componentNode);
}
}
return $componentListNode;
}
/**
* Generate doi_data element - this is what assigns the DOI
* @param $doc XMLNode
* @param $DOI string
* @param $url string
* @param $galleys array
*/
function &_generateDOIdataDom(&$doc, $DOI, $url, $galleys = null) {
$journal =& $this->getJournal();
$request = Application::getRequest();
$DOIdataNode =& XMLCustomWriter::createElement($doc, 'doi_data');
XMLCustomWriter::createChildWithText($doc, $DOIdataNode, 'doi', $DOI);
XMLCustomWriter::createChildWithText($doc, $DOIdataNode, 'resource', $url);
/* article galleys */
if ($galleys) {
// iParadigms collection element
foreach ($galleys as $galley) {
$collectionNode = XMLCustomWriter::createElement($doc, 'collection');
XMLCustomWriter::setAttribute($collectionNode, 'property', 'crawler-based');
XMLCustomWriter::appendChild($DOIdataNode, $collectionNode);
$itemNode = XMLCustomWriter::createElement($doc, 'item');
XMLCustomWriter::setAttribute($itemNode, 'crawler', 'iParadigms');
XMLCustomWriter::appendChild($collectionNode, $itemNode);
$resourceNode = XMLCustomWriter::createElement($doc, 'resource');
XMLCustomWriter::appendChild($itemNode, $resourceNode);
$urlNode = XMLCustomWriter::createTextNode($doc, $request->url($journal->getPath(), 'article', 'viewFile', array($galley->getArticleId(), $galley->getBestGalleyId($journal))));
XMLCustomWriter::appendChild($resourceNode, $urlNode);
}
// end iParadigms
// text-mining collection element
$collectionNode = XMLCustomWriter::createElement($doc, 'collection');
XMLCustomWriter::setAttribute($collectionNode, 'property', 'text-mining');
XMLCustomWriter::appendChild($DOIdataNode, $collectionNode);
foreach ($galleys as $galley) {
$itemNode = XMLCustomWriter::createElement($doc, 'item');
XMLCustomWriter::appendChild($collectionNode, $itemNode);
$resourceNode = XMLCustomWriter::createElement($doc, 'resource');
XMLCustomWriter::appendChild($itemNode, $resourceNode);
$remoteGalleyURL = $galley->getRemoteURL();
if (!$remoteGalleyURL) {
XMLCustomWriter::setAttribute($resourceNode, 'mime_type', $galley->getFileType());
}
$urlNode = XMLCustomWriter::createTextNode($doc, $request->url($journal->getPath(), 'article', 'viewFile', array($galley->getArticleId(), $galley->getBestGalleyId($journal))));
XMLCustomWriter::appendChild($resourceNode, $urlNode);
}
// end text-mining
}
return $DOIdataNode;
}
/**
* Generate author node
* @param $doc XMLNode
* @param $author Author
* @return XMLNode
*/
function &_generateAuthorDom(&$doc, &$author, $isFirst = false) {
$authorNode =& XMLCustomWriter::createElement($doc, 'person_name');
XMLCustomWriter::setAttribute($authorNode, 'contributor_role', 'author');
/* there should only be 1 primary contact per article */
if ($isFirst) {
XMLCustomWriter::setAttribute($authorNode, 'sequence', 'first');
} else {
XMLCustomWriter::setAttribute($authorNode, 'sequence', 'additional');
}
XMLCustomWriter::createChildWithText($doc, $authorNode, 'given_name', ucfirst($author->getFirstName()).(($author->getMiddleName())?' '.ucfirst($author->getMiddleName()):''));
XMLCustomWriter::createChildWithText($doc, $authorNode, 'surname', ucfirst($author->getLastName()));
if ($author->getData('orcid')) {
XMLCustomWriter::createChildWithText($doc, $authorNode, 'ORCID', $author->getData('orcid'));
}
return $authorNode;
}
/**
* Generate publisher date - order matters
* @param $doc XMLNode
* @param $pubdate string
* @return XMLNode
*/
function &_generatePublisherDateDom(&$doc, $pubdate) {
$publicationDateNode =& XMLCustomWriter::createElement($doc, 'publication_date');
XMLCustomWriter::setAttribute($publicationDateNode, 'media_type', 'online');
$parsedPubdate = strtotime($pubdate);
XMLCustomWriter::createChildWithText($doc, $publicationDateNode, 'month', date('m', $parsedPubdate), false);
XMLCustomWriter::createChildWithText($doc, $publicationDateNode, 'day', date('d', $parsedPubdate), false);
XMLCustomWriter::createChildWithText($doc, $publicationDateNode, 'year', date('Y', $parsedPubdate));
return $publicationDateNode;
}
}
?>