PubMedExportPlugin.inc.php

<?php
 
import('lib.pkp.classes.plugins.ImportExportPlugin');
 
class PubMedExportPlugin extends ImportExportPlugin {
   function register($category, $path, $mainContextId = null) {
      $success = parent::register($category, $path, $mainContextId);
      $this->addLocaleData();
      return $success;
   }
 
   function getName() {
      return 'PubMedExportPlugin';
   }
 
   function getDisplayName() {
      return __('plugins.importexport.pubmed.displayName');
   }
 
   function getDescription() {
      return __('plugins.importexport.pubmed.description');
   }
 
   function display($args, $request) {
      parent::display($args, $request);
      $templateMgr = TemplateManager::getManager($request);
      $context = $request->getContext();
      switch (array_shift($args)) {
         case 'index':
         case '':
            $apiUrl = $request->getDispatcher()->url($request, ROUTE_API, $context->getPath(), 'submissions');
            $submissionsListPanel = new \APP\components\listPanels\SubmissionsListPanel(
               'submissions',
               __('common.publications'),
               [
                  'apiUrl' => $apiUrl,
                  'count' => 100,
                  'getParams' => new stdClass(),
                  'lazyLoad' => true,
               ]
            );
            $submissionsConfig = $submissionsListPanel->getConfig();
            $submissionsConfig['addUrl'] = '';
            $submissionsConfig['filters'] = array_slice($submissionsConfig['filters'], 1);
            $templateMgr->setState([
               'components' => [
                  'submissions' => $submissionsConfig,
               ],
            ]);
            $templateMgr->assign([
               'pageComponent' => 'ImportExportPage',
            ]);
            $templateMgr->display($this->getTemplateResource('index.tpl'));
            break;
         case 'exportSubmissions':
            $exportXml = $this->exportSubmissions(
               (array) $request->getUserVar('selectedSubmissions'),
               $request->getContext(),
               $request->getUser()
            );
            import('lib.pkp.classes.file.FileManager');
            $fileManager = new FileManager();
            $exportFileName = $this->getExportFileName($this->getExportPath(), 'articles', $context, '.xml');
            $fileManager->writeFile($exportFileName, $exportXml);
            $fileManager->downloadByPath($exportFileName);
            $fileManager->deleteByPath($exportFileName);
            break;
         case 'exportIssues':
            $exportXml = $this->exportIssues(
               (array) $request->getUserVar('selectedIssues'),
               $request->getContext(),
               $request->getUser()
            );
            import('lib.pkp.classes.file.FileManager');
            $fileManager = new FileManager();
            $exportFileName = $this->getExportFileName($this->getExportPath(), 'issues', $context, '.xml');
            $fileManager->writeFile($exportFileName, $exportXml);
            $fileManager->downloadByPath($exportFileName);
            $fileManager->deleteByPath($exportFileName);
            break;
         default:
            $dispatcher = $request->getDispatcher();
            $dispatcher->handle404();
      }
   }
 
   function getPluginSettingsPrefix() {
      return 'pubmed';
   }
 
   function exportSubmissions($submissionIds, $context, $user) {
      $submissionDao = DAORegistry::getDAO('SubmissionDAO'); /* @var $submissionDao SubmissionDAO */
      $filterDao = DAORegistry::getDAO('FilterDAO'); /* @var $filterDao FilterDAO */
      $pubmedExportFilters = $filterDao->getObjectsByGroup('article=>pubmed-xml');
      assert(count($pubmedExportFilters) == 1); // Assert only a single serialization filter
      $exportFilter = array_shift($pubmedExportFilters);
      $submissions = array();
      foreach ($submissionIds as $submissionId) {
         $submission = $submissionDao->getById($submissionId);
         if ($submission && $submission->getData('contextId') == $context->getId()) $submissions[] = $submission;
      }
      libxml_use_internal_errors(true);
      $submissionXml = $exportFilter->execute($submissions, true);
      $xml = $submissionXml->saveXml();
      $errors = array_filter(libxml_get_errors(), function($a) {
         return $a->level == LIBXML_ERR_ERROR || $a->level == LIBXML_ERR_FATAL;
      });
      if (!empty($errors)) {
         $this->displayXMLValidationErrors($errors, $xml);
      }
      return $xml;
   }
 
   function exportIssues($issueIds, $context, $user) {
      $filterDao = DAORegistry::getDAO('FilterDAO'); /* @var $filterDao FilterDAO */
      $pubmedExportFilters = $filterDao->getObjectsByGroup('article=>pubmed-xml');
      assert(count($pubmedExportFilters) == 1); // Assert only a single serialization filter
      $exportFilter = array_shift($pubmedExportFilters);
      $submissionsIterator = Services::get('submission')->getMany([
         'contextId' => $context->getId(),
         'issueIds' => $issueIds,
      ]);
      libxml_use_internal_errors(true);
      $submissionXml = $exportFilter->execute(iterator_to_array($submissionsIterator), true);
      $xml = $submissionXml->saveXml();
      $errors = array_filter(libxml_get_errors(), function($a) {
         return $a->level == LIBXML_ERR_ERROR || $a->level == LIBXML_ERR_FATAL;
      });
      if (!empty($errors)) {
         $this->displayXMLValidationErrors($errors, $xml);
      }
      return $xml;
   }
 
   function executeCLI($scriptName, &$args) {
//    $command = array_shift($args);
      $xmlFile = array_shift($args);
      $journalPath = array_shift($args);
 
      $journalDao = DAORegistry::getDAO('JournalDAO'); /* @var $journalDao JournalDAO */
      $issueDao = DAORegistry::getDAO('IssueDAO'); /* @var $issueDao IssueDAO */
 
      $journal = $journalDao->getByPath($journalPath);
 
      if (!$journal) {
         if ($journalPath != '') {
            echo __('plugins.importexport.pubmed.cliError') . "\n";
            echo __('plugins.importexport.pubmed.error.unknownJournal', array('journalPath' => $journalPath)) . "\n\n";
         }
         $this->usage($scriptName);
         return;
      }
 
      if ($xmlFile != '') switch (array_shift($args)) {
         case 'articles':
            $articleSearch = new ArticleSearch();
            $results = $articleSearch->formatResults($args);
            if (!$this->exportArticles($results, $xmlFile)) {
               echo __('plugins.importexport.pubmed.cliError') . "\n";
               echo __('plugins.importexport.pubmed.export.error.couldNotWrite', array('fileName' => $xmlFile)) . "\n\n";
            }
            return;
         case 'issue':
            $issueId = array_shift($args);
            $issue = $issueDao->getByBestId($issueId, $journal->getId());
            if ($issue == null) {
               echo __('plugins.importexport.pubmed.cliError') . "\n";
               echo __('plugins.importexport.pubmed.export.error.issueNotFound', array('issueId' => $issueId)) . "\n\n";
               return;
            }
            $issues = array($issue);
            if (!$this->exportIssues($journal, $issues, $xmlFile)) {
               echo __('plugins.importexport.pubmed.cliError') . "\n";
               echo __('plugins.importexport.pubmed.export.error.couldNotWrite', array('fileName' => $xmlFile)) . "\n\n";
            }
            return;
      }
      $this->usage($scriptName);
 
   }
 
   function usage($scriptName) {
      echo __('plugins.importexport.pubmed.cliUsage', array(
         'scriptName' => $scriptName,
         'pluginName' => $this->getName()
      )) . "\n";
   }
}