DataciteExportPlugin.inc.php

<?php
 
import('classes.plugins.DOIPubIdExportPlugin');
 
// DataCite API
define('DATACITE_API_RESPONSE_OK', 201);
define('DATACITE_API_URL', 'https://mds.datacite.org/');
 
// Test DOI prefix
define('DATACITE_API_TESTPREFIX', '10.5072');
 
// Export file types.
define('DATACITE_EXPORT_FILE_XML', 0x01);
define('DATACITE_EXPORT_FILE_TAR', 0x02);
 
 
class DataciteExportPlugin extends DOIPubIdExportPlugin {
 
   function getName() {
      return 'DataciteExportPlugin';
   }
 
   function getDisplayName() {
      return __('plugins.importexport.datacite.displayName');
   }
 
   function getDescription() {
      return __('plugins.importexport.datacite.description');
   }
 
   function getSubmissionFilter() {
      return 'article=>datacite-xml';
   }
 
   function getIssueFilter() {
      return 'issue=>datacite-xml';
   }
 
   function getRepresentationFilter() {
      return 'galley=>datacite-xml';
   }
 
   function getPluginSettingsPrefix() {
      return 'datacite';
   }
 
   function getSettingsFormClassName() {
      return 'DataciteSettingsForm';
   }
 
   function getExportDeploymentClassName() {
      return 'DataciteExportDeployment';
   }
 
   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);
      }
   }
 
   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));
      if ($this->isTestMode($context)) {
         $doi = PKPString::regexp_replace('#^[^/]+/#', DATACITE_API_TESTPREFIX . '/', $doi);
      }
      $url = $this->_getObjectUrl($request, $context, $object);
      assert(!empty($url));
 
      // Prepare HTTP session.
      import('lib.pkp.classes.helpers.PKPCurlHelper');
      $curlCh = PKPCurlHelper::getCurlObject();
 
      curl_setopt($curlCh, CURLOPT_RETURNTRANSFER, true);
      curl_setopt($curlCh, CURLOPT_POST, true);
      // Set up basic authentication.
      $username = $this->getSetting($context->getId(), 'username');
      $password = $this->getSetting($context->getId(), 'password');
      curl_setopt($curlCh, CURLOPT_HTTPAUTH, CURLAUTH_BASIC);
      curl_setopt($curlCh, CURLOPT_USERPWD, "$username:$password");
      // Transmit meta-data.
      assert(is_readable($filename));
      $payload = file_get_contents($filename);
      assert($payload !== false && !empty($payload));
      curl_setopt($curlCh, CURLOPT_URL, DATACITE_API_URL . 'metadata');
      curl_setopt($curlCh, CURLOPT_HTTPHEADER, array('Content-Type: application/xml;charset=UTF-8'));
      curl_setopt($curlCh, CURLOPT_POSTFIELDS, $payload);
      $result = true;
      $response = curl_exec($curlCh);
      if ($response === false) {
         $result = array(array('plugins.importexport.common.register.error.mdsError', "Registering DOI $doi: No response from server."));
      } else {
         $status = curl_getinfo($curlCh, CURLINFO_HTTP_CODE);
         if ($status != DATACITE_API_RESPONSE_OK) {
            $result = array(array('plugins.importexport.common.register.error.mdsError', "Registering DOI $doi: $status - $response"));
         }
      }
      // Mint a DOI.
      if ($result === true) {
         $payload = "doi=$doi\nurl=$url";
         curl_setopt($curlCh, CURLOPT_URL, DATACITE_API_URL . 'doi');
         curl_setopt($curlCh, CURLOPT_HTTPHEADER, array('Content-Type: text/plain;charset=UTF-8'));
         curl_setopt($curlCh, CURLOPT_POSTFIELDS, $payload);
         $response = curl_exec($curlCh);
         if ($response === false) {
            $result = array(array('plugins.importexport.common.register.error.mdsError', 'Registering DOI $doi: No response from server.'));
         } else {
            $status = curl_getinfo($curlCh, CURLINFO_HTTP_CODE);
            if ($status != DATACITE_API_RESPONSE_OK) {
               $result = array(array('plugins.importexport.common.register.error.mdsError', "Registering DOI $doi: $status - $response"));
            }
         }
      }
      curl_close($curlCh);
      if ($result === true) {
         $object->setData($this->getDepositStatusSettingName(), EXPORT_STATUS_REGISTERED);
         $this->saveRegisteredDoi($context, $object, DATACITE_API_TESTPREFIX);
      }
      return $result;
   }
 
   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;
      }
   }
 
   function _checkForTar() {
      $tarBinary = Config::getVar('cli', 'tar');
      if (empty($tarBinary) || !is_executable($tarBinary)) {
         $result = array(
            array('manager.plugins.tarCommandNotFound')
         );
      } else {
         $result = true;
      }
      return $result;
   }
 
   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);
   }
 
   function _getObjectUrl($request, $context, $object) {
      $router = $request->getRouter();
      // Retrieve the article of article files.
      if (is_a($object, 'ArticleGalley')) {
         $articleId = $object->getSubmissionId();
         $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;
   }
 
}