Texture crossref reference support and create galley support for OJS 3.3

TexturePlugin.inc.php

@@ -102,7 +102,7 @@ public function callbackLoadHandler($hookName, $args) {
 			case 'texture/media':
 				define('HANDLER_CLASS', 'TextureHandler');
 				define('TEXTURE_PLUGIN_NAME', $this->getName());
-				$args[2] = $this->getPluginPath() . '/' . 'TextureHandler.inc.php';
+				$args[2] = $this->getPluginPath() .DIRECTORY_SEPARATOR.'controllers'.DIRECTORY_SEPARATOR. 'TextureHandler.inc.php';
 				break;
 		}
 
@@ -137,12 +137,12 @@ public function templateFetchCallback($hookName, $params) {
 				if (strtolower($fileExtension) == 'text/xml') {
 					import('lib.pkp.classes.linkAction.request.OpenWindowAction');
 					$this->_editWithTextureAction($row, $dispatcher, $request, $submissionFile, $stageId);
-					//$this->_createGalleyAction($row, $dispatcher, $request, $submissionFile, $stageId, $fileStage);
-					//$this->_exportAction($row, $dispatcher, $request, $submissionFile, $stageId, $fileStage);
+					$this->_createGalleyAction($row, $dispatcher, $request, $submissionFile, $stageId, $fileStage);
+					#$this->_exportAction($row, $dispatcher, $request, $submissionFile, $stageId, $fileStage);
 				} elseif (strtolower($fileExtension) == TEXTURE_DAR_FILE_TYPE) {
-					$this->_extractAction($row, $dispatcher, $request, $submissionFile, $stageId, $fileStage, TEXTURE_DAR_FILE_TYPE);
+				//	$this->_extractAction($row, $dispatcher, $request, $submissionFile, $stageId, $fileStage, TEXTURE_DAR_FILE_TYPE);
 				} elseif (strtolower($fileExtension) == TEXTURE_ZIP_FILE_TYPE) {
-					$this->_extractAction($row, $dispatcher, $request, $submissionFile, $stageId, $fileStage, TEXTURE_ZIP_FILE_TYPE);
+				//	$this->_extractAction($row, $dispatcher, $request, $submissionFile, $stageId, $fileStage, TEXTURE_ZIP_FILE_TYPE);
 				} elseif (strtolower($fileExtension) == TEXTURE_HTML_FILE_TYPE) {
 					import('lib.pkp.classes.linkAction.request.OpenWindowAction');
 					$this->_createGalleyAction($row, $dispatcher, $request, $submissionFile, $stageId, $fileStage);

classes/JATS.inc.php

@@ -0,0 +1,194 @@
+<?php
+
+
+use DAORegistry;
+use DOMDocument;
+use DOMXpath;
+use PKPString;
+
+class JATS extends \DOMDocument
+{
+
+	public static function getJournalMeta(DOMDocument $origDocument, $context): void
+	{
+
+		$xpath = new DOMXpath($origDocument);
+
+		$journalMeta = $xpath->query("//article/front/journal-meta");
+		foreach ($journalMeta as $journalMetaEntry) {
+			$origDocument->documentElement->removeChild($journalMetaEntry);
+		}
+		$articleMeta = $xpath->query("//article/front/article-meta");
+		if (count($articleMeta) == 1) {
+			if (count($journalMeta) == 0) {
+
+				$journalMeta = $origDocument->createElement('journal-meta');
+
+				$journalIdType = $origDocument->createElement('journal-id', $context->getLocalizedAcronym());
+				$journalIdType->setAttribute('journal-id-type', 'publisher-id');
+				$journalMeta->appendChild($journalIdType);
+				$issn = $origDocument->createElement('issn', $context->getData('onlineIssn'));
+				$issn->setAttribute('pub-type', 'epub');
+				$journalMeta->appendChild($issn);
+				$publisher = $origDocument->createElement('publisher');
+				$publisherName = $origDocument->createElement('publisher-name', $context->getData('publisherInstitution'));
+				$publisher->appendChild($publisherName);
+				$journalMeta->appendChild($publisher);
+
+				$articleMeta->item(0)->parentNode->insertBefore($journalMeta, $articleMeta->item(0));
+
+			}
+
+		}
+	}
+
+
+	public static function getArticleMetaHistory(DOMDocument $origDocument, Submission $submission, $datePublished = null): void
+	{
+
+		$xpath = new DOMXpath($origDocument);
+
+		$editDecisionDao = DAORegistry::getDAO('EditDecisionDAO');
+		$history = $xpath->query("//article/front/article-meta/history");
+
+		foreach ($history as $item) {
+			$item->parentNode->removeChild($item);
+		}
+		$history = $origDocument->createElement('history');
+		$dateReceived = $submission->getData('dateSubmitted');
+		if ($dateReceived) {
+			$dateReceived = self::getDate($origDocument, $dateReceived, 'received');
+			$history->appendChild($dateReceived);
+		}
+
+		$dateAccepted = null;
+		$decisions = $editDecisionDao->getEditorDecisions($submission->getId());
+		foreach ($decisions as $decision) {
+			if ($decision['stageId'] == WORKFLOW_STAGE_ID_EXTERNAL_REVIEW && $decision['decision'] == SUBMISSION_EDITOR_DECISION_ACCEPT)
+				$dateAccepted = $decision['dateDecided'];
+		}
+		if ($dateAccepted) {
+			$history->appendChild(self::getDate($origDocument, $dateAccepted, 'accepted'));
+		}
+
+		if ($datePublished) {
+			$history->appendChild(self::getDate($origDocument, $datePublished, 'published'));
+		}
+
+
+		$articleMeta = $xpath->query("//article/front/article-meta");
+		if ($articleMeta)
+			$articleMeta->item(0)->appendChild($history);
+
+
+	}
+
+
+	public static function getJournalMetaPubDate(DOMDocument $origDocument, $context, $submission, $datePublished,  $firstPage = null, $lastPage=null): void
+	{
+		$xpath = new DOMXpath($origDocument);
+		$timestamp = strtotime($datePublished);
+
+			$issueDao = DAORegistry::getDAO('IssueDAO');
+
+		$pubDate = $xpath->query("//article/front/article-meta/pub-date");
+
+		foreach ($pubDate as $item) {
+			$item->parentNode->removeChild($item);
+		}
+
+		$pubDate = $origDocument->createElement('pub-date');
+		$pubDate->setAttribute('pub-type','epub');
+		$day = $origDocument->createElement('day', date('d', $timestamp));
+		$pubDate->appendChild($day);
+		$month = $origDocument->createElement('month', date('m', $timestamp));
+		$pubDate->appendChild($month);
+		$year = $origDocument->createElement('year', date('Y', $timestamp));
+		$pubDate->appendChild($year);
+
+		$issue = $issueDao->getBySubmissionId($submission->getId(), $context->getId());
+		$volume = $origDocument->createElement('volume', $issue->getVolume());
+		$pubDate->appendChild($volume);
+
+		if ($firstPage) {
+			$pubDate->appendChild($origDocument->createElement('fpage',$firstPage));
+		}
+		if ($lastPage) {
+			$pubDate->appendChild($origDocument->createElement('lpage',$lastPage));
+		}
+		$articleMeta = $xpath->query("//article/front/article-meta");
+		if ($articleMeta)
+			$articleMeta->item(0)->appendChild($pubDate);
+
+
+	}
+
+
+	public static function getArticleMetaCCBYLicense(DOMDocument $origDocument, $context, $copyrightYear = null): void
+	{
+
+
+		$xpath = new DOMXpath($origDocument);
+		$permissions = $xpath->query("//article/front/article-meta/permissions");
+		foreach ($permissions as $permission) {
+			$origDocument->documentElement->removeChild($permission);
+		}
+
+
+		$articleMeta = $xpath->query("//article/front/article-meta");
+		$licenseUrl = $context->getData('licenseUrl');
+		if (count($articleMeta) > 0 and $licenseUrl) {
+
+
+			PKPString::regexp_match_get('/http[s]?:(www\.)?\/\/creativecommons.org\/licenses\/([a-z]+(-[a-z]+)*)\/(\d.0)\/*([a-z]*).*/i', $licenseUrl, $matches);
+			if (count($matches) > 5 and $matches[2] and $matches[4]) {
+
+				if (!$$copyrightYear) $copyrightYear = date('Y');
+
+				$permissionNode = $origDocument->createElement('permissions');
+				$copyrightStatementNode = $origDocument->createElement('copyright-statement', '© ' . $copyrightYear . ' The Author(s)');
+				$permissionNode->appendChild($copyrightStatementNode);
+				$copyrightYearNode = $origDocument->createElement('copyright-year', $copyrightYear);
+				$permissionNode->appendChild($copyrightYearNode);
+
+				$copyrightLicenseNode = $origDocument->createElement('copyright-license');
+				$copyrightLicenseNode->setAttribute('license-type', 'open-access');
+				$copyrightLicenseNode->setAttribute('xlink:href', $licenseUrl);
+				$copyrightLicenseNode->setAttribute('xml:lang', 'en');
+
+				$copyrightLicensePNode = $origDocument->createElement('license-p');
+
+				$inlineGraphicNode = $origDocument->createElement('inline-graphic');
+				$inlineGraphicNode->setAttribute('xlink:href', 'https://mirrors.creativecommons.org/presskit/buttons/88x31/svg/' . $matches[2] . '.svg');
+				$copyrightLicensePNode->appendChild($inlineGraphicNode);
+
+				$countryCode = $matches[5] ? strtoupper($matches[5]) : '';
+				$isoCodes = new \Sokil\IsoCodes\IsoCodesFactory();
+				$country = $isoCodes->getCountries()->getByAlpha2($countryCode) ? $isoCodes->getCountries()->getByAlpha2($countryCode)->getName() : '';
+				$licensePTextNode = $origDocument->createTextNode("This work is published under the Creative Commons  {$country} License {$matches[4]} (CC BY {$matches[4]} {$countryCode}).");
+
+				$copyrightLicensePNode->appendChild($licensePTextNode);
+				$copyrightLicenseNode->appendChild($copyrightLicensePNode);
+				$permissionNode->appendChild($copyrightLicenseNode);
+				$articleMeta[0]->appendChild($permissionNode);
+			}
+		}
+
+	}
+
+	public static function getDate(\DOMDocument $origDocument, string $dateAndTime, $type =null): DOMElement
+	{
+		$timestamp = strtotime($dateAndTime);
+		$date = $origDocument->createElement('date');
+		if ($type)	$date->setAttribute('type', $type);
+		$date->setAttribute('iso-8601-date', date('Y-m-d', $timestamp));
+		$day = $origDocument->createElement('day', date('d', $timestamp));
+		$date->appendChild($day);
+		$month = $origDocument->createElement('month', date('m', $timestamp));
+		$date->appendChild($month);
+		$year = $origDocument->createElement('year', date('Y', $timestamp));
+		$date->appendChild($year);
+		return $date;
+
+	}
+}

TextureHandler.inc.php → controllers/TextureHandler.inc.php

@@ -96,7 +96,7 @@ public function extract($args, $request) {
 		$user = $request->getUser();
 		$zipType = $request->getUserVar("zipType");
 		$submissionFile = $this->getAuthorizedContextObject(ASSOC_TYPE_SUBMISSION_FILE);
-		$archivePath = sys_get_temp_dir() . DIRECTORY_SEPARATOR . 'texture-' . $zipType . '-archive' . mt_rand();
+		$archivePath = '';//TextureHandler . inc . 'texture-' . $zipType . '-archive' . mt_rand();
 		$image_types = array('gif', 'jpg', 'jpeg', 'png', 'jpe');
 		$html_types = array('html');
 
@@ -110,7 +110,7 @@ public function extract($args, $request) {
 			$genreDAO = DAORegistry::getDAO('GenreDAO');
 			$genre = $genreDAO->getByKey('SUBMISSION', $submission->getData('contextId'));
 			$fileStage = $submissionFile->getFileStage();
-			$sourceFileId = $submissionFile->getData('submissionFileId');
+			$sourceFileId = $submissionFile->getData('fileId');
 			if ($zipType == TEXTURE_DAR_FILE_TYPE) {
 				$manifestFileDom = new DOMDocument();
 				$darManifestFilePath = $archivePath . DIRECTORY_SEPARATOR . DAR_MANIFEST_FILE;
@@ -559,7 +559,7 @@ public function json($args, $request) {
 
 
 				} elseif (!empty($resources) && isset($resources[DAR_MANUSCRIPT_FILE]) && is_object($resources[DAR_MANUSCRIPT_FILE])) {
-					$this->_updateManuscriptFile($request, $resources, $submission, $submissionFile);
+					$this->updateManuscriptFile($request, $resources, $submission, $submissionFile);
 				} else {
 					return new JSONMessage(false);
 				}
@@ -579,7 +579,7 @@ public function json($args, $request) {
 	 * @param $submissionFile SubmissionFile
 	 * @return SubmissionFile
 	 */
-	protected function _updateManuscriptFile($request, $resources, $submission, $submissionFile) {
+	protected function updateManuscriptFile($request, $resources, $submission, $submissionFile) {
 
 		$modifiedDocument = new DOMDocument('1.0', 'utf-8');
 		$modifiedData = $resources[DAR_MANUSCRIPT_FILE]->data;
@@ -593,6 +593,9 @@ protected function _updateManuscriptFile($request, $resources, $submission, $sub
 		$origDocument = new DOMDocument('1.0', 'utf-8');
 		$origDocument->loadXML($manuscriptXml);
 
+
+
+
 		$body = $origDocument->documentElement->getElementsByTagName('body')->item(0);
 		$origDocument->documentElement->removeChild($body);