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View File Name : DataciteExportPlugin.inc.php

<?php

/**
 * @file plugins/importexport/datacite/DataciteExportPlugin.inc.php
 *
 * Copyright (c) 2014-2021 Simon Fraser University
 * Copyright (c) 2003-2021 John Willinsky
 * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
 *
 * @class DataciteExportPlugin
 * @ingroup plugins_importexport_datacite
 *
 * @brief DataCite export/registration plugin.
 */

import('classes.plugins.DOIPubIdExportPlugin');

// DataCite API
define('DATACITE_API_RESPONSE_OK', 201);
define('DATACITE_API_URL', 'https://mds.datacite.org/');
define('DATACITE_API_URL_TEST', 'https://mds.test.datacite.org/');

// Export file types.
define('DATACITE_EXPORT_FILE_XML', 0x01);
define('DATACITE_EXPORT_FILE_TAR', 0x02);


class DataciteExportPlugin extends DOIPubIdExportPlugin {

	/**
	 * @see Plugin::getName()
	 */
	function getName() {
		return 'DataciteExportPlugin';
	}

	/**
	 * @see Plugin::getDisplayName()
	 */
	function getDisplayName() {
		return __('plugins.importexport.datacite.displayName');
	}

	/**
	 * @see Plugin::getDescription()
	 */
	function getDescription() {
		return __('plugins.importexport.datacite.description');
	}

	/**
	 * @copydoc PubObjectsExportPlugin::getSubmissionFilter()
	 */
	function getSubmissionFilter() {
		return 'article=>datacite-xml';
	}

	/**
	 * @copydoc PubObjectsExportPlugin::getIssueFilter()
	 */
	function getIssueFilter() {
		return 'issue=>datacite-xml';
	}

	/**
	 * @copydoc PubObjectsExportPlugin::getRepresentationFilter()
	 */
	function getRepresentationFilter() {
		return 'galley=>datacite-xml';
	}

	/**
	 * @copydoc ImportExportPlugin::getPluginSettingsPrefix()
	 */
	function getPluginSettingsPrefix() {
		return 'datacite';
	}

	/**
	 * @copydoc DOIPubIdExportPlugin::getSettingsFormClassName()
	 */
	function getSettingsFormClassName() {
		return 'DataciteSettingsForm';
	}

	/**
	 * @copydoc PubObjectsExportPlugin::getExportDeploymentClassName()
	 */
	function getExportDeploymentClassName() {
		return 'DataciteExportDeployment';
	}

	/**
	 * @copydoc PubObjectsExportPlugin::executeExportAction()
	 */
	function executeExportAction($request, $objects, $filter, $tab, $objectsFileNamePart, $noValidation = null) {
		$context = $request->getContext();
		$path = array('plugin', $this->getName());

		import('lib.pkp.classes.file.FileManager');
		$fileManager = new FileManager();

		// Export
		if ($request->getUserVar(EXPORT_ACTION_EXPORT)) {
			$result = $this->_checkForTar();
			if ($result === true) {
				$exportedFiles = array();
				foreach ($objects as $object) {
					// Get the XML
					$exportXml = $this->exportXML($object, $filter, $context, $noValidation);
					// Write the XML to a file.
					// export file name example: datacite-20160723-160036-articles-1-1.xml
					$objectFileNamePart = $objectsFileNamePart . '-' . $object->getId();
					$exportFileName = $this->getExportFileName($this->getExportPath(), $objectFileNamePart, $context, '.xml');
					$fileManager->writeFile($exportFileName, $exportXml);
					$exportedFiles[] = $exportFileName;
				}
				// If we have more than one export file we package the files
				// up as a single tar before going on.
				assert(count($exportedFiles) >= 1);
				if (count($exportedFiles) > 1) {
					// tar file name: e.g. datacite-20160723-160036-articles-1.tar.gz
					$finalExportFileName = $this->getExportFileName($this->getExportPath(), $objectFileNamePart, $context, '.tar.gz');
					$this->_tarFiles($this->getExportPath(), $finalExportFileName, $exportedFiles);
					// remove files
					foreach ($exportedFiles as $exportedFile) {
						$fileManager->deleteByPath($exportedFile);
					}
				} else {
					$finalExportFileName = array_shift($exportedFiles);
				}
				$fileManager->downloadByPath($finalExportFileName);
				$fileManager->deleteByPath($finalExportFileName);
			} else {
				if (is_array($result)) {
					foreach($result as $error) {
						assert(is_array($error) && count($error) >= 1);
						$this->_sendNotification(
							$request->getUser(),
							$error[0],
							NOTIFICATION_TYPE_ERROR,
							(isset($error[1]) ? $error[1] : null)
						);
					}
				}
				// redirect back to the right tab
				$request->redirect(null, null, null, $path, null, $tab);
			}
		} elseif ($request->getUserVar(EXPORT_ACTION_DEPOSIT)) {
			$resultErrors = array();
			foreach ($objects as $object) {
				// Get the XML
				$exportXml = $this->exportXML($object, $filter, $context, $noValidation);
				// Write the XML to a file.
				// export file name example: datacite-20160723-160036-articles-1-1.xml
				$objectFileNamePart = $objectsFileNamePart . '-' . $object->getId();
				$exportFileName = $this->getExportFileName($this->getExportPath(), $objectFileNamePart, $context, '.xml');
				$fileManager->writeFile($exportFileName, $exportXml);
				// Deposit the XML file.
				$result = $this->depositXML($object, $context, $exportFileName);
				if (is_array($result)) {
					$resultErrors[] = $result;
				}
				// Remove all temporary files.
				$fileManager->deleteByPath($exportFileName);
			}
			// send notifications
			if (empty($resultErrors)) {
				$this->_sendNotification(
					$request->getUser(),
					$this->getDepositSuccessNotificationMessageKey(),
					NOTIFICATION_TYPE_SUCCESS
				);
			} else {
				foreach($resultErrors as $errors) {
					foreach ($errors as $error) {
						assert(is_array($error) && count($error) >= 1);
						$this->_sendNotification(
							$request->getUser(),
							$error[0],
							NOTIFICATION_TYPE_ERROR,
							(isset($error[1]) ? $error[1] : null)
						);
					}
				}
			}
			// redirect back to the right tab
			$request->redirect(null, null, null, $path, null, $tab);
		} else {
			return parent::executeExportAction($request, $objects, $filter, $tab, $objectsFileNamePart);
		}
	}

	/**
	 * @copydoc PubObjectsExportPlugin::depositXML()
	 */
	function depositXML($object, $context, $filename) {
		$request = Application::get()->getRequest();
		// Get the DOI and the URL for the object.
		$doi = $object->getStoredPubId('doi');
		assert(!empty($doi));
		$testDOIPrefix = null;
		if ($this->isTestMode($context)) {
			$testDOIPrefix = $this->getSetting($context->getId(), 'testDOIPrefix');
			assert(!empty($testDOIPrefix));
			$doi = PKPString::regexp_replace('#^[^/]+/#', $testDOIPrefix . '/', $doi);
		}
		$url = $this->_getObjectUrl($request, $context, $object);
		assert(!empty($url));

		$dataCiteAPIUrl = DATACITE_API_URL;
		$username = $this->getSetting($context->getId(), 'username');
		$password = $this->getSetting($context->getId(), 'password');
		if ($this->isTestMode($context)) {
			$dataCiteAPIUrl = DATACITE_API_URL_TEST;
			$username = $this->getSetting($context->getId(), 'testUsername');
			$password = $this->getSetting($context->getId(), 'testPassword');
		}

		// Prepare HTTP session.
		assert(is_readable($filename));
		$httpClient = Application::get()->getHttpClient();
		try {
			$response = $httpClient->request('POST', $dataCiteAPIUrl . 'metadata', [
				'auth' => [$username, $password],
				'body' => fopen($filename, 'r'),
				'headers' => [
					'Content-Type' => 'application/xml;charset=UTF-8',
				],
			]);
		} catch (GuzzleHttp\Exception\RequestException $e) {
			$returnMessage = $e->getMessage();
			if ($e->hasResponse()) {
				$returnMessage = $e->getResponse()->getBody(true) . ' (' .$e->getResponse()->getStatusCode() . ' ' . $e->getResponse()->getReasonPhrase() . ')';
			}
			return [['plugins.importexport.common.register.error.mdsError', "Registering DOI $doi: $returnMessage"]];
		}

		// Mint a DOI.
		$httpClient = Application::get()->getHttpClient();
		try {
			$response = $httpClient->request('POST', $dataCiteAPIUrl . 'doi', [
				'auth' => [$username, $password],
				'headers' => [
					'Content-Type' => 'text/plain;charset=UTF-8',
				],
				'body' => "doi=$doi\nurl=$url",
			]);
		} catch (GuzzleHttp\Exception\RequestException $e) {
			$returnMessage = $e->getMessage();
			if ($e->hasResponse()) {
				$returnMessage = $e->getResponse()->getBody(true) . ' (' .$e->getResponse()->getStatusCode() . ' ' . $e->getResponse()->getReasonPhrase() . ')';
			}
			return [['plugins.importexport.common.register.error.mdsError', "Registering DOI $doi: $returnMessage"]];
		}
		$object->setData($this->getDepositStatusSettingName(), EXPORT_STATUS_REGISTERED);
		$this->saveRegisteredDoi($context, $object, $testDOIPrefix);
		return true;
	}

	/**
	 * @copydoc PKPImportExportPlugin::executeCLI()
	 */
	function executeCLICommand($scriptName, $command, $context, $outputFile, $objects, $filter, $objectsFileNamePart) {
		import('lib.pkp.classes.file.FileManager');
		$fileManager = new FileManager();
		switch ($command) {
			case 'export':
				$result = $this->_checkForTar();
				if ($result === true) {
					$exportedFiles = array();
					foreach ($objects as $object) {
						// Get the XML
						$exportXml = $this->exportXML($object, $filter, $context);
						// Write the XML to a file.
						// export file name example: datacite-20160723-160036-articles-1-1.xml
						$objectFileNamePart = $objectsFileNamePart . '-' . $object->getId();
						$exportFileName = $this->getExportFileName($this->getExportPath(), $objectFileNamePart, $context, '.xml');
						$fileManager->writeFile($exportFileName, $exportXml);
						$exportedFiles[] = $exportFileName;
					}
					// If we have more than one export file we package the files
					// up as a single tar before going on.
					assert(count($exportedFiles) >= 1);
					if (count($exportedFiles) > 1) {
						// tar file name: e.g. datacite-20160723-160036-articles-1.tar.gz
						$finalExportFileName = $this->getExportFileName($this->getExportPath(), $objectFileNamePart, $context, '.tar.gz');
						$finalExportFileType = DATACITE_EXPORT_FILE_TAR;
						$this->_tarFiles($this->getExportPath(), $finalExportFileName, $exportedFiles);
					} else {
						$finalExportFileName = array_shift($exportedFiles);
						$finalExportFileType = DATACITE_EXPORT_FILE_XML;
					}
					$outputFileExtension = ($finalExportFileType == DATACITE_EXPORT_FILE_TAR ? '.tar.gz' : '.xml');
					if (substr($outputFile , -strlen($outputFileExtension)) != $outputFileExtension) {
						$outputFile  .= $outputFileExtension;
					}
					$fileManager->copyFile($finalExportFileName, $outputFile);
					foreach ($exportedFiles as $exportedFile) {
						$fileManager->deleteByPath($exportedFile);
					}
					$fileManager->deleteByPath($finalExportFileName);
				} else {
					echo __('plugins.importexport.common.cliError') . "\n";
					echo __('manager.plugins.tarCommandNotFound') . "\n\n";
					$this->usage($scriptName);
				}
				break;
			case 'register':
				$resultErrors = array();
				foreach ($objects as $object) {
					// Get the XML
					$exportXml = $this->exportXML($object, $filter, $context);
					// Write the XML to a file.
					// export file name example: datacite-20160723-160036-articles-1-1.xml
					$objectFileNamePart = $objectsFileNamePart . '-' . $object->getId();
					$exportFileName = $this->getExportFileName($this->getExportPath(), $objectFileNamePart, $context, '.xml');
					$fileManager->writeFile($exportFileName, $exportXml);
					// Deposit the XML file.
					$result = $this->depositXML($object, $context, $exportFileName);
					if (is_array($result)) {
						$resultErrors[] = $result;
					}
					// Remove all temporary files.
					$fileManager->deleteByPath($exportFileName);
				}
				if (empty($resultErrors)) {
					echo __('plugins.importexport.common.register.success') . "\n";
				} else {
					echo __('plugins.importexport.common.cliError') . "\n";
					foreach($resultErrors as $errors) {
						foreach ($errors as $error) {
							assert(is_array($error) && count($error) >= 1);
							$errorMessage = __($error[0], array('param' => (isset($error[1]) ? $error[1] : null)));
							echo "*** $errorMessage\n";
						}
					}
					echo "\n";
					$this->usage($scriptName);
				}
				break;
		}
	}

	/**
	 * Test whether the tar binary is available.
	 * @return boolean|array Boolean true if available otherwise
	 *  an array with an error message.
	 */
	function _checkForTar() {
		$tarBinary = Config::getVar('cli', 'tar');
		if (empty($tarBinary) || !is_executable($tarBinary)) {
			$result = array(
				array('manager.plugins.tarCommandNotFound')
			);
		} else {
			$result = true;
		}
		return $result;
	}

	/**
	 * Create a tar archive.
	 * @param $targetPath string
	 * @param $targetFile string
	 * @param $sourceFiles array
	 */
	function _tarFiles($targetPath, $targetFile, $sourceFiles) {
		assert((boolean) $this->_checkForTar());
		// GZip compressed result file.
		$tarCommand = Config::getVar('cli', 'tar') . ' -czf ' . escapeshellarg($targetFile);
		// Do not reveal our internal export path by exporting only relative filenames.
		$tarCommand .= ' -C ' . escapeshellarg($targetPath);
		// Do not reveal our webserver user by forcing root as owner.
		$tarCommand .= ' --owner 0 --group 0 --';
		// Add each file individually so that other files in the directory
		// will not be included.
		foreach($sourceFiles as $sourceFile) {
			assert(dirname($sourceFile) . '/' === $targetPath);
			if (dirname($sourceFile) . '/' !== $targetPath) continue;
			$tarCommand .= ' ' . escapeshellarg(basename($sourceFile));
		}
		// Execute the command.
		exec($tarCommand);
	}

	/**
	 * Get the canonical URL of an object.
	 * @param $request Request
	 * @param $context Context
	 * @param $object Issue|Submission|ArticleGalley
	 */
	function _getObjectUrl($request, $context, $object) {
		$router = $request->getRouter();
		// Retrieve the article of article files.
		if (is_a($object, 'ArticleGalley')) {
			$publication = Services::get('publication')->get($object->getData('publicationId'));
			$articleId = $publication->getData('submissionId');
			$cache = $this->getCache();
			if ($cache->isCached('articles', $articleId)) {
				$article = $cache->get('articles', $articleId);
			} else {
				$article = Services::get('submission')->get($articleId);
			}
			assert(is_a($article, 'Submission'));
		}
		$url = null;
		switch (true) {
			case is_a($object, 'Issue'):
				$url = $router->url($request, $context->getPath(), 'issue', 'view', $object->getBestIssueId(), null, null, true);
				break;
			case is_a($object, 'Submission'):
				$url = $router->url($request, $context->getPath(), 'article', 'view', $object->getBestId(), null, null, true);
				break;
			case is_a($object, 'ArticleGalley'):
				$url = $router->url($request, $context->getPath(), 'article', 'view', array($article->getBestId(), $object->getBestGalleyId()), null, null, true);
				break;
		}
		if ($this->isTestMode($context)) {
			// Change server domain for testing.
			$url = PKPString::regexp_replace('#://[^\s]+/index.php#', '://example.com/index.php', $url);
		}
		return $url;
	}

}