tripal_jbrowse.module

<?php

/**
 * @file
 * Provides a jbrowse instance entity type.
 */

use Drupal\Core\Render\Element;
use Drupal\tripal_jbrowse\Entity\JbrowseInstance;
use Drupal\user\UserInterface;

/**
 * Implements hook_theme().
 */
function tripal_jbrowse_theme() {
  return [
    'jbrowse_instance' => [
      'render element' => 'elements',
    ],
  ];
}

/**
 * Prepares variables for jbrowse instance templates.
 *
 * Default template: jbrowse-instance.html.twig.
 *
 * @param array $variables
 *   An associative array containing:
 *   - elements: An associative array containing the jbrowse instance information and any
 *     fields attached to the entity.
 *   - attributes: HTML attributes for the containing element.
 */
function template_preprocess_jbrowse_instance(array &$variables) {
  $variables['view_mode'] = $variables['elements']['#view_mode'];
  foreach (Element::children($variables['elements']) as $key) {
    $variables['content'][$key] = $variables['elements'][$key];
  }
  $variables['#attached']['library'][] = 'tripal_jbrowse/react';
  $variables['#attached']['library'][] = 'tripal_jbrowse/jbrowse';
  $variables['#attached']['library'][] = 'tripal_jbrowse/createJBrowseLinearGenomeView';

  // Grab the URL and the starting location (sequence coordinates) of our JBrowse instance 
  // from the content entity
  // We are taking this approach rather than through content so that we are not vulnerable
  // to a user disabling it through the managed display UI
  $instance = $variables['elements']['#jbrowse_instance'];
  $url = $instance->get('jbrowse_url')->getValue();
  $variables['#attached']['drupalSettings']['jbrowseUrl'] = $url[0]['value'];
  // Location is not required so check that there is a value first
  if ($instance->get('location')->getValue()) {
    $location = $instance->get('location')->getValue();
    $variables['#attached']['drupalSettings']['location'] = $location[0]['value'];
  }

  // Add our URL as an ajax trusted URL
  $variables['#attached']['drupalSettings']['ajaxTrustedUrl'][$url[0]['value']] = TRUE;
}

/**
 * Implements hook_user_cancel().
 */
function tripal_jbrowse_user_cancel($edit, UserInterface $account, $method) {
  switch ($method) {
    case 'user_cancel_reassign':
      // Anonymize jbrowse instances.
      $storage = \Drupal::entityTypeManager()->getStorage('jbrowse_instance');
      $jbrowse_instance_ids = $storage->getQuery()
        ->condition('uid', $account->id())
        ->execute();
      foreach ($storage->loadMultiple($jbrowse_instance_ids) as $jbrowse_instance) {
        $jbrowse_instance->setOwnerId(0);
        $jbrowse_instance->save();
      }
      break;
  }
}

/**
 * Implements hook_ENTITY_TYPE_predelete() for user entities.
 */
function tripal_jbrowse_user_predelete(UserInterface $account) {
  // Delete jbrowse instances.
  $storage = \Drupal::entityTypeManager()->getStorage('jbrowse_instance');
  $jbrowse_instance_ids = $storage->getQuery()
    ->condition('uid', $account->id())
    ->execute();
  $jbrowse_instances = $storage->loadMultiple($jbrowse_instance_ids);
  $storage->delete($jbrowse_instances);
}