OAIMetadataFormat_OpenAIRE.php

<?php

/**
 * @defgroup oai_format_jats
 */

/**
 * @file OAIMetadataFormat_OpenAIRE.inc.php
 *
 * Copyright (c) 2013-2020 Simon Fraser University
 * Copyright (c) 2003-2023 John Willinsky
 * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
 *
 * @class OAIMetadataFormat_OpenAIRE
 * @ingroup oai_format
 * @see OAI
 *
 * @brief OAI metadata format class -- OpenAIRE
 */

namespace APP\plugins\generic\openAIRE;

use APP\core\Application;
use PKP\core\PKPString;
use PKP\oai\OAIMetadataFormat;
use PKP\plugins\PluginRegistry;
use PKP\plugins\Hook;
use PKP\db\DAORegistry;
use PKP\submission\GenreDAO;

class OAIMetadataFormat_OpenAIRE extends OAIMetadataFormat {

	/**
	 * @see OAIMetadataFormat#toXml
	 */
	function toXml($record, $format = null) {
		$request = Application::get()->getRequest();
		$article = $record->getData('article');
		$journal = $record->getData('journal');
		$section = $record->getData('section');
		$issue = $record->getData('issue');
		$galleys = $record->getData('galleys');
		$articleId = $article->getId();
		$publication = $article->getCurrentPublication();
		$abbreviation = $journal->getLocalizedSetting('abbreviation');
		$printIssn = $journal->getSetting('printIssn');
		$onlineIssn = $journal->getSetting('onlineIssn');
		$articleLocale = $article->getLocale();
		$publisherInstitution = $journal->getSetting('publisherInstitution');
		$datePublished = $article->getDatePublished();
		$articleDoi = $article->getStoredPubId('doi');
		$accessRights = $this->_getAccessRights($journal, $issue, $article);
		$resourceType = ($section->getData('resourceType') ? $section->getData('resourceType') : 'http://purl.org/coar/resource_type/c_6501'); # COAR resource type URI, defaults to "journal article"
		if (!$datePublished) $datePublished = $issue->getDatePublished();
		if ($datePublished) $datePublished = strtotime($datePublished);
		$parentPlugin = PluginRegistry::getPlugin('generic', 'openaireplugin');

		$response = "
		<article 
			dtd-version=\"1.1\" 
			xmlns:xlink=\"http://www.w3.org/1999/xlink\" 
			xmlns:mml=\"http://www.w3.org/1998/Math/MathML\" 
			xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" 
			xmlns:ali=\"http://www.niso.org/schemas/ali/1.0\" 
			xmlns=\"https://jats.nlm.nih.gov/publishing/1.1/\" 
			article-type=\"" . htmlspecialchars($this->_mapCoarResourceTypeToJatsArticleType($resourceType)) . "\" 
			xml:lang=\"" . substr($articleLocale, 0, 2) . "\">
		<front>
		<journal-meta>
			<journal-id journal-id-type=\"ojs\">" . htmlspecialchars($journal->getPath()) . "</journal-id>
			<journal-title-group>
			<journal-title xml:lang=\"" . substr($journal->getPrimaryLocale(), 0, 2) . "\">" . htmlspecialchars($journal->getName($journal->getPrimaryLocale())) . "</journal-title>\n";
		// Translated journal titles
		foreach ($journal->getName(null) as $locale => $title) {
			if ($locale == $journal->getPrimaryLocale()) continue;
			$response .= "\t\t\t<trans-title-group xml:lang=\"" . substr($locale, 0, 2) . "\"><trans-title>" . htmlspecialchars($title) . "</trans-title></trans-title-group>\n";
		}
		$response .= ($journal->getAcronym($journal->getPrimaryLocale())?"\t\t\t<abbrev-journal-title xml:lang=\"" . substr($journal->getPrimaryLocale(), 0, 2) . "\">" . htmlspecialchars($journal->getAcronym($journal->getPrimaryLocale())) . "</abbrev-journal-title>":'');		
		$response .= "\n\t\t\t</journal-title-group>\n";

		$response .=
			(!empty($onlineIssn)?"\t\t\t<issn pub-type=\"epub\">" . htmlspecialchars($onlineIssn) . "</issn>\n":'') .
			(!empty($printIssn)?"\t\t\t<issn pub-type=\"ppub\">" . htmlspecialchars($printIssn) . "</issn>\n":'') .
			($publisherInstitution != ''?"\t\t\t<publisher><publisher-name>" . htmlspecialchars($publisherInstitution) . "</publisher-name></publisher>\n":'') .
			"\t\t</journal-meta>\n" .
			"\t\t<article-meta>\n" .
			"\t\t\t<article-id pub-id-type=\"publisher-id\">" . $article->getId() . "</article-id>\n" . 
			(!empty($articleDoi)?"\t\t\t<article-id pub-id-type=\"doi\">" . htmlspecialchars($articleDoi) . "</article-id>\n":'') .
			"\t\t\t<article-categories><subj-group xml:lang=\"" . $journal->getPrimaryLocale() . "\" subj-group-type=\"heading\"><subject>" . htmlspecialchars($section->getLocalizedTitle()) . "</subject></subj-group></article-categories>\n" .
			"\t\t\t<title-group>\n" .
			"\t\t\t\t<article-title xml:lang=\"" . substr($articleLocale, 0, 2) . "\">" . htmlspecialchars(strip_tags($article->getTitle($articleLocale))) . "</article-title>\n";
		if (!empty($subtitle = $article->getSubtitle($articleLocale))) $response .= "\t\t\t\t<subtitle xml:lang=\"" . substr($articleLocale, 0, 2) . "\">" . htmlspecialchars($subtitle) . "</subtitle>\n";

		// Translated article titles
		foreach ($article->getTitle(null) as $locale => $title) {
			if ($locale == $articleLocale) continue;
			if ($title){
				$response .= "\t\t\t\t<trans-title-group xml:lang=\"" . substr($locale, 0, 2) . "\">\n";
				$response .= "\t\t\t\t\t<trans-title>" . htmlspecialchars(strip_tags($title)) . "</trans-title>\n";
				if (!empty($subtitle = $article->getSubtitle($locale))) $response .= "\t\t\t\t\t<trans-subtitle>" . htmlspecialchars($subtitle) . "</trans-subtitle>\n";
				$response .= "\t\t\t\t\t</trans-title-group>\n";
			}
		}
		$response .=
			"\t\t\t</title-group>\n" .
			"\t\t\t<contrib-group content-type=\"author\">\n";

		// Authors
		$affiliations = array();
		foreach ($article->getCurrentPublication()->getData('authors') as $author) {
			$affiliation = $author->getLocalizedAffiliation();
			$affiliationToken = array_search($affiliation, $affiliations);
			if ($affiliation && !$affiliationToken) {
				$affiliationToken = 'aff-' . (count($affiliations)+1);
				$affiliations[$affiliationToken] = $affiliation;
			}
			$response .=
				"\t\t\t\t<contrib " . ($author->getPrimaryContact()?'corresp="yes" ':'') . ">\n" .
				"\t\t\t\t\t<name name-style=\"western\">\n" .
				"\t\t\t\t\t\t<surname>" . htmlspecialchars(method_exists($author, 'getLastName')?$author->getLastName():$author->getLocalizedFamilyName()) . "</surname>\n" .
				"\t\t\t\t\t\t<given-names>" . htmlspecialchars(method_exists($author, 'getFirstName')?$author->getFirstName():$author->getLocalizedGivenName()) . (((method_exists($author, 'getMiddleName') && $s = $author->getMiddleName()) != '')?" $s":'') . "</given-names>\n" .
				"\t\t\t\t\t</name>\n" .
				($affiliationToken?"\t\t\t\t\t<xref ref-type=\"aff\" rid=\"$affiliationToken\" />\n":'') .
				($author->getOrcid()?"\t\t\t\t\t<contrib-id contrib-id-type=\"orcid\" authenticated=\"true\">" . htmlspecialchars($author->getOrcid()) . "</contrib-id>\n":'') .
				"\t\t\t\t</contrib>\n";
		}
		$response .= "\t\t\t</contrib-group>\n";
		foreach ($affiliations as $affiliationToken => $affiliation) {
			$response .= "\t\t\t<aff id=\"$affiliationToken\"><institution content-type=\"orgname\">" . htmlspecialchars($affiliation) . "</institution></aff>\n";
		}

		// Publication date
		if ($datePublished) $response .=
			"\t\t\t<pub-date date-type=\"pub\" publication-format=\"epub\">\n" .
			"\t\t\t\t<day>" . strftime('%d', $datePublished) . "</day>\n" .
			"\t\t\t\t<month>" . strftime('%m', $datePublished) . "</month>\n" .
			"\t\t\t\t<year>" . strftime('%Y', $datePublished) . "</year>\n" .
			"\t\t\t</pub-date>\n";

		// Issue details
		if ($issue->getVolume() && $issue->getShowVolume())
			$response .= "\t\t\t<volume>" . htmlspecialchars($issue->getVolume()) . "</volume>\n";
		if ($issue->getNumber() && $issue->getShowNumber())
			$response .= "\t\t\t<issue>" . htmlspecialchars($issue->getNumber()) . "</issue>\n";

		// Page info, if available and parseable.
		$pageInfo = $this->_getPageInfo($article);
		if ($pageInfo){
			$response .=
				"\t\t\t\t<fpage>" . $pageInfo['fpage'] . "</fpage>\n" .
				"\t\t\t\t<lpage>" . $pageInfo['lpage'] . "</lpage>\n";
		}

		// Fetch funding data from other plugins if available
		$fundingReferences = null;
		Hook::call('OAIMetadataFormat_OpenAIRE::findFunders', [&$articleId, &$fundingReferences]);
		if ($fundingReferences){
			$response .= $fundingReferences;
		}

		// Copyright, license and other permissions
		$copyrightYear = $article->getCopyrightYear();
		$copyrightHolder = $article->getLocalizedCopyrightHolder();
		$licenseUrl = $article->getLicenseURL();
		$ccBadge = Application::get()->getCCLicenseBadge($licenseUrl);
		$openAccessDate = null;
		if ($accessRights == 'embargoedAccess') {
			$openAccessDate = date('Y-m-d', strtotime($issue->getOpenAccessDate()));
		}		
		if ($copyrightYear || $copyrightHolder || $licenseUrl || $ccBadge || $openAccessDate || $accessRights == "openAccess" ) $response .=
			"\t\t\t<permissions>\n" .
			(($copyrightYear||$copyrightHolder)?"\t\t\t\t<copyright-statement>" . htmlspecialchars(__('submission.copyrightStatement', array('copyrightYear' => $copyrightYear, 'copyrightHolder' => $copyrightHolder))) . "</copyright-statement>\n":'') .			
			($copyrightYear?"\t\t\t\t<copyright-year>" . htmlspecialchars($copyrightYear) . "</copyright-year>\n":'') .
			($copyrightHolder?"\t\t\t\t<copyright-holder>" . htmlspecialchars($copyrightHolder) . "</copyright-holder>\n":'') .
			($licenseUrl?"\t\t\t\t<license xlink:href=\"" . htmlspecialchars($licenseUrl) . "\">\n" .
				($ccBadge?"\t\t\t\t\t<license-p>" . strip_tags($ccBadge) . "</license-p>\n":'') .
			"\t\t\t\t</license>\n":'') . 
			($openAccessDate?"\t\t\t\t<ali:free_to_read xmlns:ali=\"http://www.niso.org/schemas/ali/1.0\" start_date=\"" . htmlspecialchars($openAccessDate) . "\" />\n":'') .
			($accessRights == "openAccess"?"\t\t\t\t<ali:free_to_read xmlns:ali=\"http://www.niso.org/schemas/ali/1.0\" />\n":'') .
			"\t\t\t</permissions>\n";

		// landing page link
		$response .= "\t\t\t<self-uri xlink:href=\"" . htmlspecialchars($request->url($journal->getPath(), 'article', 'view', $article->getBestArticleId())) . "\" />\n";

		// full text links
		$galleys = $article->getGalleys();
		$primaryGalleys = array();
		if ($galleys) {
			$genreDao = DAORegistry::getDAO('GenreDAO');
			$primaryGenres = $genreDao->getPrimaryByContextId($journal->getId())->toArray();
			$primaryGenreIds = array_map(function($genre) {
				return $genre->getId();
			}, $primaryGenres);
			foreach ($galleys as $galley) {
				$remoteUrl = $galley->getRemoteURL();
				$file = $galley->getFile();
				if (!$remoteUrl && !$file) {
					continue;
				}
				if ($remoteUrl || in_array($file->getGenreId(), $primaryGenreIds)) {
					$response .= "\t\t\t<self-uri content-type=\"" . $galley->getFileType() . "\" xlink:href=\"" . htmlspecialchars($request->url($journal->getPath(), 'article', 'download', array($article->getBestArticleId(), $galley->getBestGalleyId()), null, null, true)) . "\" />\n";
				}
			}
		}

		// Keywords
		$subjects = array();
		if (is_array($article->getSubject(null))) foreach ($article->getSubject(null) as $locale => $subject) {
			$s = array_map('trim', explode(';', $subject));
			if (!empty($s)) $subjects[$locale] = $s;
		}
		if (!empty($subjects)) foreach ($subjects as $locale => $s) {
			$response .= "\t\t\t<kwd-group xml:lang=\"" . substr($locale, 0, 2) . "\">\n";
			foreach ($s as $subject) $response .= "\t\t\t\t<kwd>" . htmlspecialchars($subject) . "</kwd>\n";
			$response .= "\t\t\t</kwd-group>\n";
		}

		$submissionKeywordDao = DAORegistry::getDAO('SubmissionKeywordDAO');
		foreach ($submissionKeywordDao->getKeywords($publication->getId(), $journal->getSupportedLocales()) as $locale => $keywords) {
			if (empty($keywords)) continue;
			// Load the article.subject locale key in possible other languages
			$response .= "\t\t\t<kwd-group xml:lang=\"" . substr($locale, 0, 2) . "\">\n";
			foreach ($keywords as $keyword) $response .= "\t\t\t\t<kwd>" . htmlspecialchars($keyword) . "</kwd>\n";
			$response .= "\t\t\t</kwd-group>\n";
		}

		// abstract
		if ($article->getAbstract($articleLocale)) {
			$abstract = PKPString::html2text($article->getAbstract($articleLocale));
			$response .= "\t\t\t<abstract xml:lang=\"" . substr($articleLocale, 0, 2) . "\"><p>" . htmlspecialchars($abstract) . "</p></abstract>\n";
		}
		// Include translated abstracts
		foreach ($article->getAbstract(null) as $locale => $abstract) {
			if ($locale == $articleLocale) continue;
			if ($abstract){
				$abstract = PKPString::html2text($abstract);
				$response .= "\t\t\t<trans-abstract xml:lang=\"" . substr($locale, 0, 2) . "\"><p>" . htmlspecialchars($abstract) . "</p></trans-abstract>\n";
			}
		}

		// Page count
		$response .=
			($pageInfo?"\t\t\t<counts><page-count count=\"" . (int) $pageInfo['pagecount'] . "\" /></counts>\n":'');

		// OpenAIRE COAR Access Rights and OpenAIRE COAR Resource Type
		$coarAccessRights = $this->_getCoarAccessRights();
		$coarResourceLabel = $parentPlugin->_getCoarResourceType($resourceType);

		if ($accessRights || $coarResourceLabel){
			$response .= "\t\t\t<custom-meta-group>\n";
			if ($accessRights) $response .=
				"\t\t\t\t<custom-meta specific-use=\"access-right\">\n" .
				"\t\t\t\t\t<meta-name>" . $coarAccessRights[$accessRights]['label'] . "</meta-name>\n" .
				"\t\t\t\t\t<meta-value>" . $coarAccessRights[$accessRights]['url'] . "</meta-value>\n" .
				"\t\t\t\t</custom-meta>\n";
			if ($coarResourceLabel) $response .=
				"\t\t\t\t<custom-meta specific-use=\"resource-type\">\n" .
				"\t\t\t\t\t<meta-name>" . $coarResourceLabel . "</meta-name>\n" .
				"\t\t\t\t\t<meta-value>" . $resourceType . "</meta-value>\n" .
				"\t\t\t\t</custom-meta>\n";
			$response .=  "\t\t\t</custom-meta-group>\n";
		}

		$response .= 
			"\t\t</article-meta>\n" .
			"\t</front>\n" .
			"</article>";

		return $response;
	}

	/**
	 * Get an associative array containing COAR Access Rights.
	 * @return array
	 */
	function _getCoarAccessRights() {
		static $coarAccessRights = array(
			'openAccess' => array('label' => 'open access', 'url' => 'http://purl.org/coar/access_right/c_abf2'),
			'embargoedAccess' => array('label' => 'embargoed access', 'url' => 'http://purl.org/coar/access_right/c_abf2'),
			'restrictedAccess' => array('label' => 'restricted access', 'url' => 'http://purl.org/coar/access_right/c_abf2'),
			'metadataOnlyAccess' => array('label' => 'metadata only access', 'url' => 'http://purl.org/coar/access_right/c_abf2')
		);
		return $coarAccessRights;
	}

	/**
	 * Get a JATS article-type string based on COAR Resource Type URI.
	 * https://jats.nlm.nih.gov/archiving/tag-library/1.1/attribute/article-type.html
	 * @param $uri string
	 * @return string
	 */
	function _mapCoarResourceTypeToJatsArticleType($uri) {
		$resourceTypes = array(
				'http://purl.org/coar/resource_type/c_6501' => 'research-article',
				'http://purl.org/coar/resource_type/c_2df8fbb1' => 'research-article',
				'http://purl.org/coar/resource_type/c_dcae04bc' => 'review-article',
				'http://purl.org/coar/resource_type/c_beb9' => 'research-article',
				'http://purl.org/coar/resource_type/c_7bab' => 'research-article',
				'http://purl.org/coar/resource_type/c_b239' => 'editorial',
				'http://purl.org/coar/resource_type/c_545b' => 'letter',
				'http://purl.org/coar/resource_type/c_93fc' => 'case-report',
				'http://purl.org/coar/resource_type/c_efa0' => 'product-review',
				'http://purl.org/coar/resource_type/c_ba08' => 'book-review',
				'http://purl.org/coar/resource_type/c_5794' => 'meeting-report',
				'http://purl.org/coar/resource_type/c_46ec' => 'dissertation',
				'http://purl.org/coar/resource_type/c_8042' => 'research-article',
				'http://purl.org/coar/resource_type/c_816b' => 'research-article'
		);
		return $resourceTypes[$uri];
	}

	/**
	 * Get an associative array containing page info
	 * @return array
	 */
	function _getPageInfo($article) {
		$matches = $pageCount = null;
		if (PKPString::regexp_match_get('/^(\d+)$/', $article->getPages(), $matches)) {
			$matchedPage = htmlspecialchars($matches[1]);
			return array('fpage' => $matchedPage, 'lpage' => $matchedPage, 'pagecount' => '1');
		} elseif (PKPString::regexp_match_get('/^[Pp][Pp]?[.]?[ ]?(\d+)$/', $article->getPages(), $matches)) {
			$matchedPage = htmlspecialchars($matches[1]);
			return array('fpage' => $matchedPage, 'lpage' => $matchedPage, 'pagecount' => '1');
		} elseif (PKPString::regexp_match_get('/^[Pp][Pp]?[.]?[ ]?(\d+)[ ]?-[ ]?([Pp][Pp]?[.]?[ ]?)?(\d+)$/', $article->getPages(), $matches)) {
			$matchedPageFrom = htmlspecialchars($matches[1]);
			$matchedPageTo = htmlspecialchars($matches[3]);
			$pageCount = $matchedPageTo - $matchedPageFrom + 1;
			return array('fpage' => $matchedPageFrom, 'lpage' => $matchedPageTo, 'pagecount' => $pageCount);
		} elseif (PKPString::regexp_match_get('/^(\d+)[ ]?-[ ]?(\d+)$/', $article->getPages(), $matches)) {
			$matchedPageFrom = htmlspecialchars($matches[1]);
			$matchedPageTo = htmlspecialchars($matches[2]);
			$pageCount = $matchedPageTo - $matchedPageFrom + 1;
			return array('fpage' => $matchedPageFrom, 'lpage' => $matchedPageTo, 'pagecount' => $pageCount);
		} else {
			return null;
		}
	}
	
	/**
	 * Get article access rights
	 * @param $journal
	 * @param $issue
	 * @param $article
	 * @return string
	 */
	function _getAccessRights($journal, $issue, $article) {
		$accessRights = null;
		if ($journal->getData('publishingMode') == PUBLISHING_MODE_OPEN) {
			$accessRights = 'openAccess';
		} else if ($journal->getData('publishingMode') == PUBLISHING_MODE_SUBSCRIPTION) {
			if ($issue->getAccessStatus() == 0 || $issue->getAccessStatus() == ISSUE_ACCESS_OPEN) {
				$accessRights = 'openAccess';
			} else if ($issue->getAccessStatus() == ISSUE_ACCESS_SUBSCRIPTION) {
				if (is_a($article, 'PublishedArticle') && $article->getAccessStatus() == ARTICLE_ACCESS_OPEN) {
					$accessRights = 'openAccess';
				} else if ($issue->getAccessStatus() == ISSUE_ACCESS_SUBSCRIPTION && $issue->getOpenAccessDate() != NULL) {
					$accessRights = 'embargoedAccess';
				} else if ($issue->getAccessStatus() == ISSUE_ACCESS_SUBSCRIPTION && $issue->getOpenAccessDate() == NULL) {
					$accessRights = 'metadataOnlyAccess';
				}
			}
		}
		if ($journal->getData('restrictSiteAccess') == 1 || $journal->getData('restrictArticleAccess') == 1) {
			$accessRights = 'restrictedAccess';
		}
		return $accessRights;
	}

}