CrossRefExportPlugin.inc.php

<?php
 
import('classes.plugins.DOIPubIdExportPlugin');
 
// The status of the Crossref DOI.
// any, notDeposited, and markedRegistered are reserved
define('CROSSREF_STATUS_FAILED', 'failed');
 
define('CROSSREF_API_DEPOSIT_OK', 200);
 
define('CROSSREF_API_URL', 'https://api.crossref.org/v2/deposits');
//TESTING
define('CROSSREF_API_URL_DEV', 'https://test.crossref.org/v2/deposits');
 
define('CROSSREF_API_STAUTS_URL', 'https://api.crossref.org/servlet/submissionDownload');
//TESTING
define('CROSSREF_API_STAUTS_URL_DEV', 'https://test.crossref.org/servlet/submissionDownload');
 
// The name of the setting used to save the registered DOI and the URL with the deposit status.
define('CROSSREF_DEPOSIT_STATUS', 'depositStatus');
 
 
class CrossRefExportPlugin extends DOIPubIdExportPlugin {
 
   function getName() {
      return 'CrossRefExportPlugin';
   }
 
   function getDisplayName() {
      return __('plugins.importexport.crossref.displayName');
   }
 
   function getDescription() {
      return __('plugins.importexport.crossref.description');
   }
 
   function getSubmissionFilter() {
      return 'preprint=>crossref-xml';
   }
 
   function getStatusNames() {
      return array_merge(parent::getStatusNames(), array(
         EXPORT_STATUS_REGISTERED => __('plugins.importexport.crossref.status.registered'),
         CROSSREF_STATUS_FAILED => __('plugins.importexport.crossref.status.failed'),
         EXPORT_STATUS_MARKEDREGISTERED => __('plugins.importexport.crossref.status.markedRegistered'),
      ));
   }
 
   function getStatusActions($pubObject) {
      $request = Application::get()->getRequest();
      $dispatcher = $request->getDispatcher();
      import('lib.pkp.classes.linkAction.request.AjaxModal');
      return array(
         CROSSREF_STATUS_FAILED =>
            new LinkAction(
               'failureMessage',
               new AjaxModal(
                  $dispatcher->url(
                     $request, ROUTE_COMPONENT, null,
                     'grid.settings.plugins.settingsPluginGridHandler',
                     'manage', null, array('plugin' => 'CrossRefExportPlugin', 'category' => 'importexport', 'verb' => 'statusMessage',
                     'batchId' => $pubObject->getData($this->getDepositBatchIdSettingName()), 'submissionId' => $pubObject->getId())
                  ),
                  __('plugins.importexport.crossref.status.failed'),
                  'failureMessage'
               ),
               __('plugins.importexport.crossref.status.failed')
            )
      );
   }
 
   function getStatusMessage($request) {
      // if the failure occured on request and the message was saved
      // return that message
      $submissionId = $request->getUserVar('submissionId');
      $submissionDao = DAORegistry::getDAO('SubmissionDAO');
      $article = $submissionDao->getById($submissionId);
      $failedMsg = $article->getData($this->getFailedMsgSettingName());
      if (!empty($failedMsg)) {
         return $failedMsg;
      }
      // else check the failure message with Crossref, using the API
      $context = $request->getContext();
 
      import('lib.pkp.classes.helpers.PKPCurlHelper');
      $curlCh = PKPCurlHelper::getCurlObject();
 
      curl_setopt($curlCh, CURLOPT_RETURNTRANSFER, true);
      curl_setopt($curlCh, CURLOPT_POST, true);
      curl_setopt($curlCh, CURLOPT_HEADER, 0);
 
      // Use a different endpoint for testing and production.
      $endpoint = ($this->isTestMode($context) ? CROSSREF_API_STAUTS_URL_DEV : CROSSREF_API_STAUTS_URL);
      curl_setopt($curlCh, CURLOPT_URL, $endpoint);
      // Set the form post fields
      $username = $this->getSetting($context->getId(), 'username');
      $password = $this->getSetting($context->getId(), 'password');
      $batchId = $request->getUserVar('batchId');
      $data = array('doi_batch_id' => $batchId, 'type' => 'result', 'usr' => $username, 'pwd' => $password);
      curl_setopt($curlCh, CURLOPT_POSTFIELDS, $data);
      $response = curl_exec($curlCh);
 
      if ($response === false) {
         $result = __('plugins.importexport.common.register.error.mdsError', array('param' => 'No response from server.'));
      } else {
         $result = $response;
      }
      return $result;
   }
 
 
   function getExportActionNames() {
      return array(
         EXPORT_ACTION_DEPOSIT => __('plugins.importexport.crossref.action.register'),
         EXPORT_ACTION_EXPORT => __('plugins.importexport.crossref.action.export'),
         EXPORT_ACTION_MARKREGISTERED => __('plugins.importexport.crossref.action.markRegistered'),
      );
   }
 
   protected function _getObjectAdditionalSettings() {
      return array_merge(parent::_getObjectAdditionalSettings(), array(
         $this->getDepositBatchIdSettingName(),
         $this->getFailedMsgSettingName(),
      ));
   }
 
   function getPluginSettingsPrefix() {
      return 'crossref';
   }
 
   function getSettingsFormClassName() {
      return 'CrossRefSettingsForm';
   }
 
   function getExportDeploymentClassName() {
      return 'CrossrefExportDeployment';
   }
 
   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();
      $resultErrors = array();
 
      if ($request->getUserVar(EXPORT_ACTION_DEPOSIT)) {
         assert($filter != null);
         // Errors occured will be accessible via the status link
         // thus do not display all errors notifications (for every article),
         // just one general.
         // Warnings occured when the registration was successfull will however be
         // displayed for each article.
         $errorsOccured = false;
         // The new Crossref deposit API expects one request per object.
         // On contrary the export supports bulk/batch object export, thus
         // also the filter expects an array of objects.
         // Thus the foreach loop, but every object will be in an one item array for
         // the export and filter to work.
         foreach ($objects as $object) {
            // Get the XML
            $exportXml = $this->exportXML(array($object), $filter, $context, $noValidation);
            // Write the XML to a file.
            // export file name example: crossref-20160723-160036-articles-1-1.xml
            $objectsFileNamePart = $objectsFileNamePart . '-' . $object->getId();
            $exportFileName = $this->getExportFileName($this->getExportPath(), $objectsFileNamePart, $context, '.xml');
            $fileManager->writeFile($exportFileName, $exportXml);
            // Deposit the XML file.
            $result = $this->depositXML($object, $context, $exportFileName);
            if (!$result) {
               $errorsOccured = true;
            }
            if (is_array($result)) {
               $resultErrors[] = $result;
            }
            // Remove all temporary files.
            $fileManager->deleteByPath($exportFileName);
         }
         // send notifications
         if (empty($resultErrors)) {
            if ($errorsOccured) {
               $this->_sendNotification(
                  $request->getUser(),
                  'plugins.importexport.crossref.register.error.mdsError',
                  NOTIFICATION_TYPE_ERROR
               );
            } else {
               $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, $tab);
      } else {
         parent::executeExportAction($request, $objects, $filter, $tab, $objectsFileNamePart, $noValidation);
      }
   }
 
   function depositOnPublish($hookName, $args) {
      error_log("depositOnPublish");
      $newPublication = $args[0];
      $objects[] = Services::get('submission')->get($newPublication->getData('submissionId'));
      $request = Application::get()->getRequest();
      $context = $request->getContext();
      $filter = $this->getSubmissionFilter();
      $objectsFileNamePart = 'preprints';
      $noValidation = null;
 
      import('lib.pkp.classes.file.FileManager');
      $fileManager = new FileManager();
      $resultErrors = array();
      $errorsOccured = false;
 
      foreach ($objects as $object) {
         $exportXml = $this->exportXML(array($object), $filter, $context, $noValidation);
         $objectsFileNamePart = $objectsFileNamePart . '-' . $object->getId();
         $exportFileName = $this->getExportFileName($this->getExportPath(), $objectsFileNamePart, $context, '.xml');
         $fileManager->writeFile($exportFileName, $exportXml);
         $result = $this->depositXML($object, $context, $exportFileName);
         if (!$result) {
            $errorsOccured = true;
         }
         if (is_array($result)) {
            $resultErrors[] = $result;
         }
         $fileManager->deleteByPath($exportFileName);
      }
      // send notifications
      if (empty($resultErrors)) {
         if ($errorsOccured) {
            $this->_sendNotification(
               $request->getUser(),
               'plugins.importexport.crossref.register.error.mdsError',
               NOTIFICATION_TYPE_ERROR
            );
         } else {
            $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)
               );
            }
         }
      }
   }
 
   function depositXML($objects, $context, $filename) {
      $status = null;
 
      import('lib.pkp.classes.helpers.PKPCurlHelper');
      $curlCh = PKPCurlHelper::getCurlObject();
 
      curl_setopt($curlCh, CURLOPT_RETURNTRANSFER, true);
      curl_setopt($curlCh, CURLOPT_POST, true);
      curl_setopt($curlCh, CURLOPT_HEADER, 0);
 
      // Use a different endpoint for testing and production.
      $endpoint = ($this->isTestMode($context) ? CROSSREF_API_URL_DEV : CROSSREF_API_URL);
      curl_setopt($curlCh, CURLOPT_URL, $endpoint);
      // Set the form post fields
      $username = $this->getSetting($context->getId(), 'username');
      $password = $this->getSetting($context->getId(), 'password');
      assert(is_readable($filename));
      if (function_exists('curl_file_create')) {
         curl_setopt($curlCh, CURLOPT_SAFE_UPLOAD, true);
         $cfile = new CURLFile($filename);
      } else {
         $cfile = "@$filename";
      }
      $data = array('operation' => 'doMDUpload', 'usr' => $username, 'pwd' => $password, 'mdFile' => $cfile);
      curl_setopt($curlCh, CURLOPT_POSTFIELDS, $data);
      $response = curl_exec($curlCh);
 
      $msg = null;
      if ($response === false) {
         $result = array(array('plugins.importexport.common.register.error.mdsError', 'No response from server.'));
      } elseif (curl_getinfo($curlCh, CURLINFO_HTTP_CODE) != CROSSREF_API_DEPOSIT_OK) {
         // These are the failures that occur immediatelly on request
         // and can not be accessed later, so we save the falure message in the DB
         $xmlDoc = new DOMDocument();
         $xmlDoc->loadXML($response);
         // Get batch ID
         $batchIdNode = $xmlDoc->getElementsByTagName('batch_id')->item(0);
         // Get re message
         $msg = $response;
         $status = CROSSREF_STATUS_FAILED;
         $result = false;
      } else {
         // Get DOMDocument from the response XML string
         $xmlDoc = new DOMDocument();
         $xmlDoc->loadXML($response);
         $batchIdNode = $xmlDoc->getElementsByTagName('batch_id')->item(0);
 
         // Get the DOI deposit status
         // If the deposit failed
         $failureCountNode = $xmlDoc->getElementsByTagName('failure_count')->item(0);
         $failureCount = (int) $failureCountNode->nodeValue;
         if ($failureCount > 0) {
            $status = CROSSREF_STATUS_FAILED;
            $result = false;
         } else {
            // Deposit was received
            $status = EXPORT_STATUS_REGISTERED;
            $result = true;
 
            // If there were some warnings, display them
            $warningCountNode = $xmlDoc->getElementsByTagName('warning_count')->item(0);
            $warningCount = (int) $warningCountNode->nodeValue;
            if ($warningCount > 0) {
               $result = array(array('plugins.importexport.crossref.register.success.warning', htmlspecialchars($response)));
            }
            // A possibility for other plugins (e.g. reference linking) to work with the response
            HookRegistry::call('crossrefexportplugin::deposited', array($this, $response, $objects));
         }
      }
      // Update the status
      if ($status) {
         $this->updateDepositStatus($context, $objects, $status, $batchIdNode->nodeValue, $msg);
         $this->updateObject($objects);
      }
 
      curl_close($curlCh);
      return $result;
   }
 
   function updateDepositStatus($context, $object, $status, $batchId, $failedMsg = null) {
      assert(is_a($object, 'Submission'));
      // remove the old failure message, if exists
      $object->setData($this->getFailedMsgSettingName(), null);
      $object->setData($this->getDepositStatusSettingName(), $status);
      $object->setData($this->getDepositBatchIdSettingName(), $batchId);
      if ($failedMsg) {
         $object->setData($this->getFailedMsgSettingName(), $failedMsg);
      }
      if ($status == EXPORT_STATUS_REGISTERED) {
         // Save the DOI -- the object will be updated
         $this->saveRegisteredDoi($context, $object);
      }
   }
 
   function markRegistered($context, $objects) {
      foreach ($objects as $object) {
         // remove the old failure message, if exists
         $object->setData($this->getFailedMsgSettingName(), null);
         $object->setData($this->getDepositStatusSettingName(), EXPORT_STATUS_MARKEDREGISTERED);
         $this->saveRegisteredDoi($context, $object);
      }
   }
 
   function getFailedMsgSettingName() {
      return $this->getPluginSettingsPrefix().'::failedMsg';
   }
 
   function getDepositBatchIdSettingName() {
      return $this->getPluginSettingsPrefix().'::batchId';
   }
 
   function getDepositSuccessNotificationMessageKey() {
      return 'plugins.importexport.common.register.success';
   }
 
   function executeCLICommand($scriptName, $command, $context, $outputFile, $objects, $filter, $objectsFileNamePart) {
      switch ($command) {
         case 'export':
            PluginRegistry::loadCategory('generic', true, $context->getId());
            $exportXml = $this->exportXML($objects, $filter, $context);
            if ($outputFile) file_put_contents($outputFile, $exportXml);
            break;
         case 'register':
            PluginRegistry::loadCategory('generic', true, $context->getId());
            import('lib.pkp.classes.file.FileManager');
            $fileManager = new FileManager();
            $resultErrors = array();
            // Errors occured will be accessible via the status link
            // thus do not display all errors notifications (for every article),
            // just one general.
            // Warnings occured when the registration was successfull will however be
            // displayed for each article.
            $errorsOccured = false;
            // The new Crossref deposit API expects one request per object.
            // On contrary the export supports bulk/batch object export, thus
            // also the filter expects an array of objects.
            // Thus the foreach loop, but every object will be in an one item array for
            // the export and filter to work.
            foreach ($objects as $object) {
               // Get the XML
               $exportXml = $this->exportXML(array($object), $filter, $context);
               // Write the XML to a file.
               // export file name example: crossref-20160723-160036-articles-1-1.xml
               $objectsFileNamePartId = $objectsFileNamePart . '-' . $object->getId();
               $exportFileName = $this->getExportFileName($this->getExportPath(), $objectsFileNamePartId, $context, '.xml');
               $fileManager->writeFile($exportFileName, $exportXml);
               // Deposit the XML file.
               $result = $this->depositXML($object, $context, $exportFileName);
               if (!$result) {
                  $errorsOccured = true;
               }
               if (is_array($result)) {
                  $resultErrors[] = $result;
               }
               // Remove all temporary files.
               $fileManager->deleteByPath($exportFileName);
            }
            // display deposit result status messages
            if (empty($resultErrors)) {
               if ($errorsOccured) {
                  echo __('plugins.importexport.crossref.register.error.mdsError') . "\n";
               } else {
                  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;
      }
   }
 
}