tripal · laceysanderson · Apr 16, 2024 · Dec 19, 2023 · Dec 19, 2023 · Dec 19, 2023
diff --git a/tripal/src/Entity/TripalEntity.php b/tripal/src/Entity/TripalEntity.php
@@ -568,10 +568,12 @@ public static function postLoad(EntityStorageInterface $storage, array &$entitie
     // `tripal_load_listing` session variable to TRUE.  If it is TRUE then
     // we skip this. @todo: in the future if we want to only attach
     // specific fields we can get more fancy.
-    $session = \Drupal::request()->getSession();
-    $is_listing = $session->get('tripal_load_listing');
-    if ($is_listing === TRUE) {
-      return;
+    if (\Drupal::request()->hasSession()) {
+      $session = \Drupal::request()->getSession();
+      $is_listing = $session->get('tripal_load_listing');
+      if ($is_listing === TRUE) {
+        return;
+      }
     }
 
     $entity_type_id = $storage->getEntityTypeId();

diff --git a/tripal/src/ListBuilders/TripalEntityListBuilder.php b/tripal/src/ListBuilders/TripalEntityListBuilder.php
@@ -58,8 +58,13 @@ public function buildRow(EntityInterface $entity) {
    * {@inheritdoc}
    */
   public function load() {
-    $session = \Drupal::request()->getSession();
-    $session->set('tripal_load_listing', TRUE);
+    // Using the session helps speed up this listing by telling TripalEntity not
+    // to load ALL the fields.
+    if (\Drupal::request()->hasSession()) {
+      $session = \Drupal::request()->getSession();
+      $session->set('tripal_load_listing', TRUE);
+    }
+
     try {
       $entity_ids = $this->getEntityIds();
       $entities = $this->storage->loadMultiple($entity_ids);

diff --git a/tripal/src/Services/TripalPublish.php b/tripal/src/Services/TripalPublish.php
@@ -14,15 +14,15 @@ class TripalPublish {
    *
    * @var integer $total_items
    */
-  private $total_items;
+  private $total_items = 0;
 
   /**
    * The number of items that have been handled so far.  This must never
    * be below 0 and never exceed $total_items;
    *
    * @var integer $num_handled
    */
-  private $num_handled;
+  private $num_handled = 0;
 
   /**
    * The interval when the job progress should be updated. Updating the job
@@ -33,7 +33,7 @@ class TripalPublish {
    *
    * @var integer $interval
    */
-  private $interval;
+  private $interval = 1;
 
   /**
    * The TripalJob object.
@@ -42,13 +42,6 @@ class TripalPublish {
    */
   protected $job = NULL;
 
-  /**
-   * The TripalLogger object.
-   *
-   * @var \Drupal\tripal\Services\TripalLogger $logger
-   */
-  protected $logger = NULL;
-
   /**
    * The id of the entity type (bundle)
    *
@@ -73,15 +66,13 @@ class TripalPublish {
    */
   protected $field_info = [];
 
-
   /**
    * Stores the bundle (entity type) object.
    *
    * @var \Drupal\tripal\Entity\TripalEntityType $entity_type
    **/
   protected $entity_type = NULL;
 
-
   /**
    * The TripalStorage object.
    *
@@ -109,14 +100,21 @@ class TripalPublish {
    *
    * @var array $unsupported_fields
    */
-  protected $unsupported_fields;
+  protected $unsupported_fields = [];
 
   /**
    * Stores the last percentage that progress was reported.
    *
    * @var integer
    */
-  protected $reported;
+  protected $reported = 0;
+
+  /**
+   * The TripalLogger object.
+   *
+   * @var \Drupal\tripal\Services\TripalLogger $logger
+   */
+  protected $logger = NULL;
 
   /**
    * Initializes the publisher service.
@@ -128,15 +126,20 @@ class TripalPublish {
    */
   public function init($bundle, $datastore, $datastore_options = [], TripalJob $job = NULL) {
 
-    $this->bundle = $bundle;
-    $this->datastore = $datastore;
-    $this->job = $job;
+    // Initialize class variables that may persist between consecutive jobs
     $this->total_items = 0;
-    $this->interval = 1;
     $this->num_handled = 0;
+    $this->interval = 1;
+    $this->job = $job;
+    $this->bundle = $bundle;
+    $this->datastore = $datastore;
+    $this->field_info = [];
+    $this->entity_type = NULL;
+    $this->storage = NULL;
+    $this->required_types = [];
+    $this->unsupported_fields = [];
     $this->reported = 0;
 
-
     // Initialize the logger.
     $this->logger = \Drupal::service('tripal.logger');
     if ($job) {
@@ -298,6 +301,7 @@ protected function setFieldInfo() {
             $field_info['prop_types'][$prop_type->getKey()] = $prop_type;
           }
           $this->field_info[$field_name] = $field_info;
+
         }
       }
     }
@@ -473,7 +477,9 @@ protected function getEntityTitles($matches) {
           $field = $this->field_info[$field_name]['instance'];
           $main_prop = $field->mainPropertyName();
           $value = $match[$field_name][$delta][$main_prop]['value']->getValue();
-          $entity_title = trim(preg_replace("/\[$field_name\]/", $value,  $entity_title));
+          if ($value !== NULL) {
+            $entity_title = trim(preg_replace("/\[$field_name\]/", $value,  $entity_title));
+          }
         }
       }
       $titles[] = $entity_title;

diff --git a/tripal/tests/src/Functional/Permissions/TripalRoutePermissionsTest.php b/tripal/tests/src/Functional/Permissions/TripalRoutePermissionsTest.php
@@ -5,6 +5,7 @@
 use Drupal\Tests\BrowserTestBase;
 use Drupal\file\Entity\File;
 use Drupal\user\Entity\Role;
+use Drupal\Core\Session;
 use Drupal\Core\Url;
 
 /**
@@ -27,6 +28,8 @@ class TripalRoutePermissionsTest extends BrowserTestBase {
    * @group Tripal Permissions
    */
   public function testTripalAdminPages() {
+    $this->assertTrue(\Drupal::request()->hasSession(),
+      'This test depends on having a session but for some reason there is not one available.');
     $session = $this->getSession();
 
     // The URLs to check with the key being the label expected in the
@@ -108,6 +111,8 @@ public function testTripalAdminPages() {
    * @group Tripal Jobs
    */
   public function testTripalJobPages() {
+    $this->assertTrue(\Drupal::request()->hasSession(),
+      'This test depends on having a session but for some reason there is not one available.');
     $session = $this->getSession();
 
     // The job to use for testing.
@@ -173,6 +178,8 @@ public function testTripalJobPages() {
    * @group Tripal Dashboard
    */
   public function testTripalDashboardPages() {
+    $this->assertTrue(\Drupal::request()->hasSession(),
+      'This test depends on having a session but for some reason there is not one available.');
     $session = $this->getSession();
 
     // The URLs to check.
@@ -232,6 +239,8 @@ public function testTripalDashboardPages() {
    * @group Tripal Content
    */
   public function testTripalContentPages() {
+    $this->assertTrue(\Drupal::request()->hasSession(),
+      'This test depends on having a session but for some reason there is not one available.');
     $session = $this->getSession();
 
     // Create a Content Type + Entity for this test.
@@ -345,6 +354,8 @@ public function testTripalContentPages() {
    */
   public function testAdminTripalDataFilesPages() {
     $session = $this->getSession();
+    $this->assertTrue(\Drupal::request()->hasSession(),
+      'This test depends on having a session but for some reason there is not one available.');
 
     // The URLs to check.
     $urls = [
@@ -398,6 +409,8 @@ public function testAdminTripalDataFilesPages() {
    * @group Tripal Data Files
    */
   public function testTripalDataFilesPages() {
+    $this->assertTrue(\Drupal::request()->hasSession(),
+      'This test depends on having a session but for some reason there is not one available.');
     $session = $this->getSession();
 
     $permission = 'manage tripal files';
@@ -476,6 +489,8 @@ public function testTripalDataFilesPages() {
    * @group Tripal Term Configuration
    */
   public function testTripalTermConfigPages() {
+    $this->assertTrue(\Drupal::request()->hasSession(),
+      'This test depends on having a session but for some reason there is not one available.');
     $session = $this->getSession();
 
     // The URLs to check.

diff --git a/tripal/tests/src/Functional/Services/TripalTokenParserTest.php b/tripal/tests/src/Functional/Services/TripalTokenParserTest.php
@@ -13,7 +13,7 @@
  *
  * @group Tripal
  * @group Tripal Services
- * @group Tripal Publish
+ * @group TripalPublish
  */
 class TripalTokenParserTest extends TripalTestBrowserBase {
 

diff --git a/tripal/tests/src/Traits/TripalTestTrait.php b/tripal/tests/src/Traits/TripalTestTrait.php
@@ -232,4 +232,78 @@ public function createTripalContentType($values = []) {
 
     return $entity_type_obj;
   }
+
+  /**
+   * Creates a content type and associated fields using the
+   * tripalentitytype_collection and tripalfield_collection configuration.
+   *
+   * @param string $config_id
+   *   The id from a tripalentitytype_collection config file. Fields will also be
+   *   added if there is a tripalfield_collection with this same id.
+   * @param string $content_type_id
+   *   The id of the content type to create. It must exist in the specified YAML.
+   *
+   * @return integer
+   *   The return value is 1 if everything went well and 2 if the content type
+   *   was created but the fields were not due to a missing config with matching
+   *   id. If the content type was not created then PHPUnit asserts fail.
+   */
+  protected function createContentTypeFromConfig($config_id, $content_type_id, $createTerms = FALSE) {
+    $content_type_service = \Drupal::service('tripal.tripalentitytype_collection');
+    $field_service = \Drupal::service('tripal.tripalfield_collection');
+    $config_factory = \Drupal::service('config.factory');
+    $idsmanager = \Drupal::service('tripal.collection_plugin_manager.idspace');
+
+    // FIRST THE CONTENT TYPE.
+    $yaml_contentTypes = 'tripal.tripalentitytype_collection.' . $config_id;
+
+    // check that config is installed.
+    $config = $config_factory->get($yaml_contentTypes);
+    $this->assertIsObject($config,
+      'You need to have called $this->installConfig for the module containing the configuration for the content type you want to use in this test.');
+    $specific_config = $config->get('content_types');
+    $this->assertIsArray($specific_config,
+      'You need to have called $this->installConfig for the module containing the configuration for the content type you want to use in this test.');
+
+    foreach ($specific_config as $content_type) {
+
+      if (!array_key_exists('id', $content_type) OR $content_type['id'] != $content_type_id) {
+        continue;
+      }
+
+      list($termIdSpace, $termAccession) = explode(':', $content_type['term']);
+      $idspace = $idsmanager->loadCollection($termIdSpace);
+      $this->assertIsObject($idspace, "We were not able to get the id space " . $termIdSpace);
+      $term =  $idspace->getTerm($termAccession);
+      $this->assertIsObject($term, "We were not able to get the term " . $content_type['term']);
+      $content_type['term'] = $term;
+
+      // Add the content type
+      $content_type = $content_type_service->createContentType($content_type);
+      $this->assertIsObject($content_type,
+        "We were not able to create the $content_type_id content type in the testing environment.");
+    }
+
+    // NOW THE FIELDS
+    $yaml_fields = 'tripal.tripalfield_collection.' . $config_id;
+
+    // check that config is installed.
+    $config = $config_factory->get($yaml_fields);
+    if (!is_object($config)) {
+      return 2;
+    }
+    $specific_config = $config->get('fields');
+    if (!is_array($specific_config)) {
+      return 2;
+    }
+
+    foreach ($specific_config as $field) {
+      if (array_key_exists('content_type', $field) AND $field['content_type'] === $content_type_id) {
+        // @debug print "\nAdding Field to Bundle: " . print_r($field,TRUE);
+        $field_service->addBundleField($field);
+      }
+    }
+
+    return 1;
+  }
 }
diff --git a/tripal_chado/tests/src/Functional/Forms/chadoInstallerFormTest.php b/tripal_chado/tests/src/Functional/Forms/chadoInstallerFormTest.php
@@ -50,6 +50,8 @@ protected function setUp(): void {
    * @group chado-install-form
    */
   public function testLoadInstallerForm() {
+    $this->assertTrue(\Drupal::request()->hasSession(),
+      'This test depends on having a session but for some reason there is not one available.');
     $session = $this->getSession();
 
     // Check that the page opens.

diff --git a/tripal_chado/tests/src/Functional/Permissions/TripalChadoRoutePermissionsTest.php b/tripal_chado/tests/src/Functional/Permissions/TripalChadoRoutePermissionsTest.php
@@ -25,6 +25,8 @@ class TripalChadoRoutePermissionsTest extends BrowserTestBase {
    *
    */
   public function testTripalChadoAdminPages() {
+    $this->assertTrue(\Drupal::request()->hasSession(),
+      'This test depends on having a session but for some reason there is not one available.');
     $session = $this->getSession();
 
     // The URLs to check with the key being the label expected in the

diff --git a/tripal_chado/tests/src/Kernel/ChadoTestKernelBase.php b/tripal_chado/tests/src/Kernel/ChadoTestKernelBase.php
@@ -3,6 +3,7 @@
 
 use Drupal\Tests\tripal\Kernel\TripalTestKernelBase;
 use Drupal\tripal\TripalDBX\TripalDbx;
+use Drupal\tripal\TripalVocabTerms\TripalTerm;
 use Drupal\tripal_chado\Database\ChadoConnection;
 use Drupal\Tests\tripal_chado\Traits\ChadoTestTrait;
 
@@ -93,5 +94,4 @@ protected function setUp() :void {
         ->save();
     }
   }
-
 }