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<?php
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/**
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* @file plugins/importexport/pubmed/PubMedExportPlugin.php
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*
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* Copyright (c) 2014-2022 Simon Fraser University
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* Copyright (c) 2003-2022 John Willinsky
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* Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
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*
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* @class PubMedExportPlugin
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*
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* @brief PubMed/MEDLINE XML metadata export plugin
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*/
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namespace APP\plugins\importexport\pubmed;
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use APP\core\Application;
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use APP\facades\Repo;
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use APP\journal\JournalDAO;
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use APP\template\TemplateManager;
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use Exception;
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use PKP\core\PKPApplication;
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use PKP\db\DAORegistry;
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use PKP\file\FileManager;
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use PKP\filter\FilterDAO;
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use PKP\plugins\ImportExportPlugin;
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class PubMedExportPlugin extends ImportExportPlugin
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{
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/**
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* @copydoc Plugin::register()
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*
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* @param null|mixed $mainContextId
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*/
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public function register($category, $path, $mainContextId = null)
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{
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$success = parent::register($category, $path, $mainContextId);
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$this->addLocaleData();
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return $success;
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}
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/**
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* Get the name of this plugin. The name must be unique within
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* its category.
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*
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* @return string name of plugin
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*/
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public function getName()
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{
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return 'PubMedExportPlugin';
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}
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/**
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* Get the display name.
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*
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* @return string
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*/
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public function getDisplayName()
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{
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return __('plugins.importexport.pubmed.displayName');
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}
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/**
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* Get the display description.
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*
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* @return string
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*/
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public function getDescription()
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{
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return __('plugins.importexport.pubmed.description');
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}
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/**
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* Display the plugin.
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*
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* @param array $args
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* @param \APP\core\Request $request
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*/
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public function display($args, $request)
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{
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parent::display($args, $request);
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$templateMgr = TemplateManager::getManager($request);
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$context = $request->getContext();
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switch (array_shift($args)) {
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case 'index':
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case '':
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$apiUrl = $request->getDispatcher()->url($request, PKPApplication::ROUTE_API, $context->getPath(), 'submissions');
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$submissionsListPanel = new \APP\components\listPanels\SubmissionsListPanel(
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'submissions',
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__('common.publications'),
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[
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'apiUrl' => $apiUrl,
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'count' => 100,
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'getParams' => new \stdClass(),
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'lazyLoad' => true,
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]
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);
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$submissionsConfig = $submissionsListPanel->getConfig();
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$submissionsConfig['addUrl'] = '';
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$submissionsConfig['filters'] = array_slice($submissionsConfig['filters'], 1);
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$templateMgr->setState([
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'components' => [
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'submissions' => $submissionsConfig,
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],
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]);
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$templateMgr->assign([
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'pageComponent' => 'ImportExportPage',
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]);
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$templateMgr->display($this->getTemplateResource('index.tpl'));
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break;
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case 'exportSubmissions':
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$exportXml = $this->exportSubmissions(
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(array) $request->getUserVar('selectedSubmissions'),
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$request->getContext(),
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$request->getUser()
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);
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$fileManager = new FileManager();
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$exportFileName = $this->getExportFileName($this->getExportPath(), 'articles', $context, '.xml');
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$fileManager->writeFile($exportFileName, $exportXml);
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$fileManager->downloadByPath($exportFileName);
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$fileManager->deleteByPath($exportFileName);
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break;
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case 'exportIssues':
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$exportXml = $this->exportIssues(
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(array) $request->getUserVar('selectedIssues'),
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$request->getContext(),
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$request->getUser()
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);
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$fileManager = new FileManager();
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$exportFileName = $this->getExportFileName($this->getExportPath(), 'issues', $context, '.xml');
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$fileManager->writeFile($exportFileName, $exportXml);
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$fileManager->downloadByPath($exportFileName);
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$fileManager->deleteByPath($exportFileName);
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break;
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default:
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$dispatcher = $request->getDispatcher();
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$dispatcher->handle404();
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}
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}
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/**
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* @copydoc ImportExportPlugin::getPluginSettingsPrefix()
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*/
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public function getPluginSettingsPrefix()
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{
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return 'pubmed';
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}
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public function exportSubmissions($submissionIds, $context, $user)
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{
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$filterDao = DAORegistry::getDAO('FilterDAO'); /** @var FilterDAO $filterDao */
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$pubmedExportFilters = $filterDao->getObjectsByGroup('article=>pubmed-xml');
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assert(count($pubmedExportFilters) == 1); // Assert only a single serialization filter
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$exportFilter = array_shift($pubmedExportFilters);
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$submissions = [];
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foreach ($submissionIds as $submissionId) {
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$submission = Repo::submission()->get($submissionId);
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if ($submission && $submission->getData('contextId') == $context->getId()) {
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$submissions[] = $submission;
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}
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}
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libxml_use_internal_errors(true);
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$submissionXml = $exportFilter->execute($submissions, true);
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$xml = $submissionXml->saveXml();
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$errors = array_filter(libxml_get_errors(), function ($a) {
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return $a->level == LIBXML_ERR_ERROR || $a->level == LIBXML_ERR_FATAL;
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});
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if (!empty($errors)) {
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$this->displayXMLValidationErrors($errors, $xml);
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}
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return $xml;
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}
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/**
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* Get the XML for a set of issues.
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*
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* @param array $issueIds Array of issue IDs
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* @param \PKP\context\Context $context
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* @param \PKP\user\User $user
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*
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* @return string XML contents representing the supplied issue IDs.
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*/
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public function exportIssues($issueIds, $context, $user)
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{
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$filterDao = DAORegistry::getDAO('FilterDAO'); /** @var FilterDAO $filterDao */
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/** @var \APP\plugins\importexport\pubmed\filter\ArticlePubMedXmlFilter[] $pubmedExportFilters */
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$pubmedExportFilters = $filterDao->getObjectsByGroup('article=>pubmed-xml');
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assert(count($pubmedExportFilters) == 1); // Assert only a single serialization filter
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$exportFilter = array_shift($pubmedExportFilters);
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$submissions = Repo::submission()
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->getCollector()
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->filterByContextIds([$context->getId()])
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->filterByIssueIds($issueIds)
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->getMany();
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libxml_use_internal_errors(true);
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$input = $submissions->toArray();
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$submissionXml = $exportFilter->execute($input, true);
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$xml = $submissionXml->saveXml();
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$errors = array_filter(libxml_get_errors(), function ($a) {
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return $a->level == LIBXML_ERR_ERROR || $a->level == LIBXML_ERR_FATAL;
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});
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if (!empty($errors)) {
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$this->displayXMLValidationErrors($errors, $xml);
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}
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return $xml;
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}
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/**
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* Execute import/export tasks using the command-line interface.
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*
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* @param array $args Parameters to the plugin
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*/
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public function executeCLI($scriptName, &$args)
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{
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// $command = array_shift($args);
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$xmlFile = array_shift($args);
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$journalPath = array_shift($args);
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$journalDao = DAORegistry::getDAO('JournalDAO'); /** @var JournalDAO $journalDao */
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$journal = $journalDao->getByPath($journalPath);
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if (!$journal) {
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if ($journalPath != '') {
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echo __('plugins.importexport.pubmed.cliError') . "\n";
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echo __('plugins.importexport.pubmed.error.unknownJournal', ['journalPath' => $journalPath]) . "\n\n";
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}
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$this->usage($scriptName);
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return;
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}
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$user = Application::get()->getRequest()->getUser();
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if ($xmlFile != '') {
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switch (array_shift($args)) {
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case 'articles':
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try {
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file_put_contents($xmlFile, $this->exportSubmissions($args, $journal, $user));
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} catch (Exception $e) {
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echo $e->getMessage() . "\n\n";
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}
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return;
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case 'issue':
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$issueId = array_shift($args);
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$issue = Repo::issue()->getByBestId($issueId, $journal->getId());
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if ($issue == null) {
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echo __('plugins.importexport.pubmed.cliError') . "\n";
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echo __('plugins.importexport.pubmed.export.error.issueNotFound', ['issueId' => $issueId]) . "\n\n";
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return;
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}
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$issues = [$issue];
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try {
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file_put_contents($xmlFile, $this->exportIssues($issues, $journal, $user));
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} catch (Exception $e) {
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echo $e->getMessage() . "\n\n";
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}
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return;
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}
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}
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$this->usage($scriptName);
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}
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/**
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* Display the command-line usage information
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*/
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public function usage($scriptName)
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{
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echo __('plugins.importexport.pubmed.cliUsage', [
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'scriptName' => $scriptName,
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'pluginName' => $this->getName()
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]) . "\n";
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}
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}
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