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File: DepositPackage.inc.php
<?php

/**
 * @file plugins/generic/pln/classes/DepositPackage.inc.php
 *
 * Copyright (c) 2013-2019 Simon Fraser University
 * Copyright (c) 2003-2019 John Willinsky
 * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
 *
 * @class DepositPackage
 * @ingroup plugins_generic_pln
 *
 * @brief Handle PLN requests
 */

import('classes.file.JournalFileManager');
import('lib.pkp.classes.scheduledTask.ScheduledTask');

class DepositPackage {

	/**
	 * @var $deposit Deposit
	 */
	var $_deposit;
	
	/**
	 * If the DepositPackage object was created as part of a scheduled task
	 * run, then save the task so error messages can be logged there.
	 * @var ScheduledTask $_task;
	 */
	var $_task;
	

	/**
	 * Constructor. 
	 * 
	 * @param $deposit Deposit
	 * @param $task ScheduledTask
	 * 
	 * @return DepositPackage
	 */
	function DepositPackage($deposit, $task = null) {
		$this->_deposit = $deposit;
		$this->_task = $task;
	}
	
	/**
	 * Send a message to a log. If the deposit package is aware of a 
	 * a scheduled task, the message will be sent to the task's 
	 * log. Otherwise it will be sent to error_log().
	 * 
	 * @param $message string Locale-specific message to be logged
	 */
	function _logMessage($message) {
		if($this->_task) {
			$this->_task->addExecutionLogEntry($message, SCHEDULED_TASK_MESSAGE_TYPE_NOTICE);
		} else {
			error_log($message);
		}
	}

	/**
	 * Get the directory used to store deposit data.
	 * @return string
	 */
	function getDepositDir() {
		$journalDao =& DAORegistry::getDAO('JournalDAO');
		$fileManager = new JournalFileManager($journalDao->getById($this->_deposit->getJournalId()));
		return $fileManager->filesDir . PLN_PLUGIN_ARCHIVE_FOLDER . DIRECTORY_SEPARATOR . $this->_deposit->getUUID();
	}

	/**
	 * Get the filename used to store the deposit's atom document.
	 * @return string
	 */
	function getAtomDocumentPath() {
		return $this->getDepositDir() . DIRECTORY_SEPARATOR . $this->_deposit->getUUID() . ".xml";
	}

	/**
	 * Get the filename used to store the deposit's bag.
	 * @return string
	 */
	 function getPackageFilePath() {
		return $this->getDepositDir() . DIRECTORY_SEPARATOR . $this->_deposit->getUUID() . ".zip";
	}
	
	/**
	 * Create a DOMElement in the $dom, and set the element name, namespace, and 
	 * content. Any invalid UTF-8 characters will be dropped. The
	 * content will be placed inside a CDATA section.
	 * 
	 * @param DOMDocument $dom
	 * @param string $elementName
	 * @param string $content
	 * @param string $namespace
	 * @return DOMElement
	 */
	function _generateElement($dom, $elementName, $content, $namespace = null){
		// remove any invalid UTF-8.
		$original = mb_substitute_character();
		mb_substitute_character(0xFFFD);
		$filtered = mb_convert_encoding($content, 'UTF-8', 'UTF-8');
		mb_substitute_character($original);
		
		// put the filtered content in a CDATA, as it may contain markup that 
		// isn't valid XML.
		$node = $dom->createCDATASection($filtered);
		$element = $dom->createElementNS($namespace, $elementName);
		$element->appendChild($node);
		return $element;
	}

	/**
	 * Create an atom document for this deposit.
	 * @return string
	 */
	function generateAtomDocument() {
		
		$plnPlugin =& PluginRegistry::getPlugin('generic',PLN_PLUGIN_NAME);
		$journalDao =& DAORegistry::getDAO('JournalDAO');
		$journal =& $journalDao->getById($this->_deposit->getJournalId());
		$fileManager = new JournalFileManager($journal);
		
		// set up folder and file locations
		$atomFile = $this->getAtomDocumentPath();
		$packageFile = $this->getPackageFilePath();
		
		// make sure our bag is present
		if (!$fileManager->fileExists($packageFile)) {
			$this->_logMessage(__("plugins.generic.pln.error.depositor.missingpackage", array('file' => $packageFile)));
			return false;
		}
		
		$atom = new DOMDocument('1.0', 'utf-8');
		$entry = $atom->createElementNS('http://www.w3.org/2005/Atom', 'entry');
		$entry->setAttributeNS('http://www.w3.org/2000/xmlns/' ,'xmlns:dcterms', 'http://purl.org/dc/terms/');
		$entry->setAttributeNS('http://www.w3.org/2000/xmlns/' ,'xmlns:pkp', 'http://pkp.sfu.ca/SWORD');
		
		$email = $this->_generateElement($atom, 'email', $journal->getSetting('contactEmail'));
		$entry->appendChild($email);
		
		$title = $this->_generateElement($atom, 'title', $journal->getLocalizedTitle());
		$entry->appendChild($title);
		
		$pkpJournalUrl = $this->_generateElement($atom, 'pkp:journal_url', $journal->getUrl(), 'http://pkp.sfu.ca/SWORD');
		$entry->appendChild($pkpJournalUrl);

		$pkpPublisher = $this->_generateElement($atom, 'pkp:publisherName', $journal->getSetting('publisherInstitution'), 'http://pkp.sfu.ca/SWORD');
		$entry->appendChild($pkpPublisher);

		$pkpPublisherUrl = $this->_generateElement($atom, 'pkp:publisherUrl', $journal->getSetting('publisherUrl'), 'http://pkp.sfu.ca/SWORD');
		$entry->appendChild($pkpPublisherUrl);

		$issn = '';
		
		if ($journal->getSetting('onlineIssn')) {
			$issn = $journal->getSetting('onlineIssn');
		} else if ($journal->getSetting('printIssn')) {
			$issn = $journal->getSetting('printIssn');
		}
		
		$pkpIssn = $this->_generateElement($atom, 'pkp:issn', $issn, 'http://pkp.sfu.ca/SWORD');
		$entry->appendChild($pkpIssn);
		
		$id = $this->_generateElement($atom, 'id', 'urn:uuid:'.$this->_deposit->getUUID());
		$entry->appendChild($id);
		
		$updated = $this->_generateElement($atom, 'updated', strftime("%FT%TZ",strtotime($this->_deposit->getDateModified())));
		$entry->appendChild($updated);
		
		$url = $journal->getUrl() . '/' . PLN_PLUGIN_ARCHIVE_FOLDER . '/deposits/' . $this->_deposit->getUUID();
		$pkpDetails = $this->_generateElement($atom, 'pkp:content', $url, 'http://pkp.sfu.ca/SWORD');
		$pkpDetails->setAttribute('size', ceil(filesize($packageFile)/1000));
		
		$objectVolume = "";
		$objectIssue = "";
		$objectPublicationDate = 0;
		
		switch ($this->_deposit->getObjectType()) {
			case PLN_PLUGIN_DEPOSIT_OBJECT_ARTICLE:
				$depositObjects = $this->_deposit->getDepositObjects();
				while ($depositObject =& $depositObjects->next()) {
					$publishedArticleDao =& DAORegistry::getDAO('PublishedArticleDAO');
					$article = $publishedArticleDao->getPublishedArticleByArticleId($depositObject->getObjectId());
					if ($article->getDatePublished() > $objectPublicationDate)
						$objectPublicationDate = $article->getDatePublished();
					unset($depositObject);
				}
				break;
			case PLN_PLUGIN_DEPOSIT_OBJECT_ISSUE:
				$depositObjects = $this->_deposit->getDepositObjects();
				while ($depositObject =& $depositObjects->next()) {
					$issueDao =& DAORegistry::getDAO('IssueDAO');
					$issue = $issueDao->getIssueById($depositObject->getObjectId());
					$objectVolume = $issue->getVolume();
					$objectIssue = $issue->getNumber();
					if ($issue->getDatePublished() > $objectPublicationDate)
						$objectPublicationDate = $issue->getDatePublished();
					unset($depositObject);
				}
				break;
		}
		
		$pkpDetails->setAttribute('volume', $objectVolume);
		$pkpDetails->setAttribute('issue', $objectIssue);
		$pkpDetails->setAttribute('pubdate', strftime("%F",strtotime($objectPublicationDate)));
		
		switch ($plnPlugin->getSetting($journal->getId(), 'checksum_type')) {
			case 'SHA-1':
				$pkpDetails->setAttribute('checksumType', 'SHA-1');
				$pkpDetails->setAttribute('checksumValue', sha1_file($packageFile));
				break;
			case 'MD5':
				$pkpDetails->setAttribute('checksumType', 'MD5');
				$pkpDetails->setAttribute('checksumValue', md5_file($packageFile));
				break;
		}

		$entry->appendChild($pkpDetails);
		$atom->appendChild($entry);

		$locale = $journal->getPrimaryLocale();
		$license = $atom->createElementNS('http://pkp.sfu.ca/SWORD', 'license');
		$license->appendChild($this->_generateElement($atom, 'openAccessPolicy', $journal->getLocalizedSetting('openAccessPolicy', $locale), 'http://pkp.sfu.ca/SWORD'));
		$license->appendChild($this->_generateElement($atom, 'licenseURL', $journal->getLocalizedSetting('licenseURL', $locale), 'http://pkp.sfu.ca/SWORD'));
		
		$mode = $atom->createElementNS('http://pkp.sfu.ca/SWORD', 'publishingMode');
		switch($journal->getSetting('publishingMode')) {
			case PUBLISHING_MODE_OPEN:
				$mode->nodeValue = 'Open';
				break;
			case PUBLISHING_MODE_SUBSCRIPTION:
				$mode->nodeValue = 'Subscription';
				break;
			case PUBLISHING_MODE_NONE:
				$mode->nodeValue = 'None';
				break;
		}
		$license->appendChild($mode);
		$license->appendChild($this->_generateElement($atom, 'copyrightNotice', $journal->getLocalizedSetting('copyrightNotice', $locale), 'http://pkp.sfu.ca/SWORD'));
		$license->appendChild($this->_generateElement($atom, 'copyrightBasis', $journal->getLocalizedSetting('copyrightBasis'), 'http://pkp.sfu.ca/SWORD'));
		$license->appendChild($this->_generateElement($atom, 'copyrightHolder', $journal->getLocalizedSetting('copyrightHolder'), 'http://pkp.sfu.ca/SWORD'));
		
		$entry->appendChild($license);
		$atom->save($atomFile);
		
		return $atomFile;
		
	}
	
	/**
	 * Create a package containing the serialized deposit objects. If the 
	 * bagit library fails to load, null will be returned.
	 * 
	 * @return string The full path of the created zip archive
	 */
	function generatePackage() {
		
		if( ! @include_once(dirname(__FILE__).'/../lib/bagit.php')) {
			$this->_logMessage(__("plugins.generic.pln.error.include.bagit"));
			return;
		}
		
		// get DAOs, plugins and settings
		$journalDao =& DAORegistry::getDAO('JournalDAO');
		$issueDao =& DAORegistry::getDAO('IssueDAO');
		$sectionDao =& DAORegistry::getDAO('SectionDAO');
		$publishedArticleDao =& DAORegistry::getDAO('PublishedArticleDAO');
		PluginRegistry::loadCategory('importexport');
		$exportPlugin =& PluginRegistry::getPlugin('importexport','NativeImportExportPlugin');
		$plnPlugin =& PluginRegistry::getPlugin('generic',PLN_PLUGIN_NAME);
		$fileManager = new JournalFileManager($journalDao->getById($this->_deposit->getJournalId()));
		
		$journal =& $journalDao->getById($this->_deposit->getJournalId());
		$depositObjects = $this->_deposit->getDepositObjects();
		
		// set up folder and file locations
		$bagDir = $this->getDepositDir() . DIRECTORY_SEPARATOR . $this->_deposit->getUUID();
		$packageFile = $this->getPackageFilePath();
		$exportFile =  tempnam(sys_get_temp_dir(), 'ojs-pln-export-');
		$termsFile =  tempnam(sys_get_temp_dir(), 'ojs-pln-terms-');
		
		$bag = new BagIt($bagDir);
		
		switch ($this->_deposit->getObjectType()) {
			case PLN_PLUGIN_DEPOSIT_OBJECT_ARTICLE:
				$articles = array();
				
				// we need to add all of the relevant articles to an array to export as a batch
				while ($depositObject =& $depositObjects->next()) {
					$article =& $publishedArticleDao->getPublishedArticleByArticleId($this->_deposit->getObjectId(), $journal->getId());
					$issue =& $issueDao->getIssueById($article->getIssueId(), $journal->getId());
					$section =& $sectionDao->getSection($article->getSectionId());
					
					// add the article to the array we'll pass for export
					$articles[] = array(
						'publishedArticle' => $article,
						'section' => $section,
						'issue' => $issue,
						'journal' => $journal
					);
					unset($depositObject);
				}
				
				// export all of the articles together
				if ($exportPlugin->exportArticles($articles, $exportFile) !== true) {
					$this->_logMessage(__("plugins.generic.pln.error.depositor.export.articles.error"));
					return false;
				}
				break;
			case PLN_PLUGIN_DEPOSIT_OBJECT_ISSUE:
			
				// we only ever do one issue at a time, so get that issue
				$depositObject =& $depositObjects->next();
				$issue =& $issueDao->getIssueByBestIssueId($depositObject->getObjectId(),$journal->getId());
				
				// export the issue
				if ($exportPlugin->exportIssue($journal, $issue, $exportFile) !== true) {
					$this->_logMessage(__("plugins.generic.pln.error.depositor.export.issue.error"));
					return false;
				}
				break;
			default:
		}
		
		// add the current terms to the bag
		$termsXml = new DOMDocument('1.0', 'utf-8');
		$entry = $termsXml->createElementNS('http://www.w3.org/2005/Atom', 'entry');
		$entry->setAttributeNS('http://www.w3.org/2000/xmlns/' ,'xmlns:dcterms', 'http://purl.org/dc/terms/');
		$entry->setAttributeNS('http://www.w3.org/2000/xmlns/' ,'xmlns:pkp', PLN_PLUGIN_NAME);

		$terms = unserialize($plnPlugin->getSetting($this->_deposit->getJournalId(), 'terms_of_use'));
		$agreement = unserialize($plnPlugin->getSetting($this->_deposit->getJournalId(), 'terms_of_use_agreement'));
		
		$pkpTermsOfUse = $termsXml->createElementNS(PLN_PLUGIN_NAME, 'pkp:terms_of_use');
		foreach ($terms as $termName => $termData) {
			$element = $termsXml->createElementNS(PLN_PLUGIN_NAME, $termName, $termData['term']);
			$element->setAttribute('updated',$termData['updated']);
			$element->setAttribute('agreed', $agreement[$termName]);
			$pkpTermsOfUse->appendChild($element);
		}

		$entry->appendChild($pkpTermsOfUse);
		$termsXml->appendChild($entry);
		$termsXml->save($termsFile);

		// add the exported content to the bag
		$bag->addFile($exportFile, $this->_deposit->getObjectType() . $this->_deposit->getUUID() . '.xml');
		// add the exported content to the bag
		$bag->addFile($termsFile, 'terms' . $this->_deposit->getUUID() . '.xml');
		$bag->update();
		
		// create the bag
		$bag->package($packageFile,'zip');
		
		// remove the temporary bag directory and temp files
		$fileManager->rmtree($bagDir);
		$fileManager->deleteFile($exportFile);
		$fileManager->deleteFile($termsFile);
		
		return $packageFile;
	}

	/**
	 * Transfer the atom document to the PLN.
	 */
	function transferDeposit() {
		$journalId = $this->_deposit->getJournalId();
		$depositDao =& DAORegistry::getDAO('DepositDAO');
		$journalDao =& DAORegistry::getDAO('JournalDAO');
		$plnPlugin =& PluginRegistry::getPlugin('generic',PLN_PLUGIN_NAME);
		$fileManager = new JournalFileManager($journalDao->getById($journalId));
		$plnDir = $fileManager->filesDir . PLN_PLUGIN_ARCHIVE_FOLDER;
		
		// post the atom document
		$url = $plnPlugin->getSetting($journalId, 'pln_network');
		if ($this->_deposit->getLockssAgreementStatus()) {
			$url .= PLN_PLUGIN_CONT_IRI . '/' . $plnPlugin->getSetting($journalId, 'journal_uuid');
			$url .= '/' . $this->_deposit->getUUID() . '/edit';
			$result = $plnPlugin->_curlPutFile(
				$url,
				$this->getAtomDocumentPath()
			);
		} else {
			$url .= PLN_PLUGIN_COL_IRI . '/' . $plnPlugin->getSetting($journalId, 'journal_uuid');
			$result = $plnPlugin->_curlPostFile(
				$url,
				$this->getAtomDocumentPath()
			);
		}
						
		// if we get the OK, set the status as transferred
		if (($result['status'] == PLN_PLUGIN_HTTP_STATUS_OK) || ($result['status'] == PLN_PLUGIN_HTTP_STATUS_CREATED)) {
			$this->_deposit->setTransferredStatus();
			// unset a remote error if this worked
			$this->_deposit->setLockssReceivedStatus(false);
			// if this was an update, unset the update flag
			$this->_deposit->setLockssAgreementStatus(false);
			$this->_deposit->setLastStatusDate(time());
			$depositDao->updateDeposit($this->_deposit);
		} else {
			// we got an error back from the staging server
			if($result['status'] == FALSE) {
				$this->_logMessage(__("plugins.generic.pln.error.network.deposit", array('error' => $result['error'])));
			} else {
				$this->_logMessage(__("plugins.generic.pln.error.http.deposit", array('error' => $result['status'])));
			}
			$this->_deposit->setLockssReceivedStatus();
			$this->_deposit->setLastStatusDate(time());
			$depositDao->updateDeposit($this->_deposit);
		}
		
	}

	/**
	 * Package a deposit for transfer to and retrieval by the PLN.
	 */
	function packageDeposit() {
				
		$depositDao =& DAORegistry::getDAO('DepositDAO');
		$journalDao =& DAORegistry::getDAO('JournalDAO');
		$fileManager = new JournalFileManager($journalDao->getById($this->_deposit->getJournalId()));
		$plnDir = $fileManager->filesDir . PLN_PLUGIN_ARCHIVE_FOLDER;
		
		// make sure the pln work directory exists
		if ($fileManager->fileExists($plnDir,'dir') !== true) { $fileManager->mkdir($plnDir); }
		
		// make a location for our work and clear it out if it's there
		$depositDir = $plnDir . DIRECTORY_SEPARATOR . $this->_deposit->getUUID();
		if ($fileManager->fileExists($depositDir,'dir')) $fileManager->rmtree($depositDir);
		$fileManager->mkdir($depositDir);
		
		$packagePath = $this->generatePackage();
		if( ! $packagePath) {
			return;
		}
		if (!$fileManager->fileExists($packagePath)) {
			$this->_deposit->setPackagedStatus(false);
			$depositDao->updateDeposit($this->_deposit);
			return;
		}
		
		if (!$fileManager->fileExists($this->generateAtomDocument())) {
			$this->_deposit->setPackagedStatus(false);
			$depositDao->updateDeposit($this->_deposit);
			return;
		}
		
		// update the deposit's status
		$this->_deposit->setPackagedStatus();
		$depositDao->updateDeposit($this->_deposit);
		
	}

	/**
	 * Update the deposit's status by checking with the PLN.
	 */
	function updateDepositStatus() {
		$journalId = $this->_deposit->getJournalID();
		$depositDao =& DAORegistry::getDAO('DepositDAO');
		$plnPlugin =& PluginRegistry::getPlugin('generic', 'plnplugin');

		$url = $plnPlugin->getSetting($journalId, 'pln_network') . PLN_PLUGIN_CONT_IRI;
		$url .= '/' . $plnPlugin->getSetting($journalId, 'journal_uuid');
		$url .= '/' . $this->_deposit->getUUID() . '/state';

		// retrieve the content document
		$result = $plnPlugin->_curlGet($url);

		if ($result['status'] != PLN_PLUGIN_HTTP_STATUS_OK) {
			// stop here if we didn't get an OK
			if($result['status'] === FALSE) {
				error_log(__('plugins.generic.pln.error.network.swordstatement', array('error' => $result['error'])));
			} else {
				error_log(__('plugins.generic.pln.error.http.swordstatement', array('error' => $result['status'])));
			}
			return;
		}

		$contentDOM = new DOMDocument();
		$contentDOM->preserveWhiteSpace = false;
		$contentDOM->loadXML($result['result']);

		// get the remote deposit state
		$processingState = $contentDOM->getElementsByTagName('category')->item(0)->getAttribute('term');
		switch ($processingState) {
			case 'depositedByJournal':
				$this->_deposit->setTransferredStatus(true);
				break;
			case 'harvested':
			case 'xml-validated':
			case 'payload-validated':
			case 'virus-checked':
				$this->_deposit->setReceivedStatus(true);
				break;
			case 'bag-validated':
			case 'reserialized':
				$this->_deposit->setValidatedStatus(true);
				break;
			case 'deposited':
				$this->_deposit->setSentStatus(true);
				break;
			default:
				$this->_logMessage('Deposit ' . $this->_deposit->getId() . ' has unknown processing state ' . $processingState);
		}
		
		$lockssState = $contentDOM->getElementsByTagName('category')->item(1)->getAttribute('term');
		switch($lockssState) {
			case '':
				// do nothing.
				break;
			case 'received':
				$this->_deposit->setLockssReceivedStatus();
				break;
			case 'syncing':
				$this->_deposit->setLockssSyncingStatus();
				break;
			case 'agreement':
				if( ! $this->_deposit->getLockssAgreementStatus()) {
					$journalDao =& DAORegistry::getDAO('JournalDAO');
					$fileManager = new JournalFileManager($journalDao->getById($this->_deposit->getJournalId()));
					$depositDir = $this->getDepositDir();
					$fileManager->rmtree($depositDir);
				}
				$this->_deposit->setLockssAgreementStatus(true);
				break;
			default:
				$this->_logMessage('Deposit ' . $this->_deposit->getId() . ' has unknown LOCKSS state ' . $processingState);
		}
		
		$this->_deposit->setLastStatusDate(time());
		$depositDao->updateDeposit($this->_deposit);
	}
}
?>