Merge branch '4.x' into tv4g1-issue1414-uo__unit

tripal/src/Form/TripalImporterForm.php

@@ -170,6 +170,23 @@ public function submitForm(array &$form, FormStateInterface $form_state) {
     $importer = $importer_manager->createInstance($plugin_id);
     $importer_def = $importer_manager->getDefinitions()[$plugin_id];
 
+    // Now allow the loader to do its own submit if needed.
+    try {
+      $importer->formSubmit($form, $form_state);
+      // Ensure any modifications made by the importer are used.
+      $form_values = $form_state->getValues();
+      $run_args = $form_values;
+    }
+    catch (\Exception $e) {
+        \Drupal::messenger()->addMessage('Cannot submit import: ' . $e->getMessage(), 'error');
+    }
+
+    // If the importer wants to rebuild the form for some reason then let's
+    // not add a job.
+    if ($form_state->isRebuilding() == TRUE) {
+      return;
+    }
+
     // Remove the file_local and file_upload args. We'll add in a new
     // full file path and the fid instead.
     unset($run_args['file_local']);
@@ -218,23 +235,8 @@ public function submitForm(array &$form, FormStateInterface $form_state) {
       $file_details['file_remote'] = $file_remote;
     }
     try {
-      // Now allow the loader to do its own submit if needed.
-      $importer->formSubmit($form, $form_state);
-      // If the formSubmit made changes to the $form_state we need to update the
-      // $run_args info.
-      if ($run_args !== $form_values) {
-        $run_args = $form_values;
-      }
-
-      // If the importer wants to rebuild the form for some reason then let's
-      // not add a job.
-      if ($form_state->isRebuilding() == TRUE) {
-        return;
-      }
-
       $importer->createImportJob($run_args, $file_details);
       $importer->submitJob();
-
     }
     catch (\Exception $e) {
         \Drupal::messenger()->addMessage('Cannot submit import: ' . $e->getMessage(), 'error');

tripal/src/TripalImporter/TripalImporterBase.php

@@ -11,11 +11,32 @@
 use Drupal\Core\Form\FormStateInterface;
 use Drupal\Core\Ajax\AjaxResponse;
 use Drupal\Core\Ajax\ReplaceCommand;
+use Drupal\Core\DependencyInjection\DependencySerializationTrait;
+
 /**
  * Defines an interface for tripal impoerter plugins.
  */
 abstract class TripalImporterBase extends PluginBase implements TripalImporterInterface {
 
+  /**
+   * Needed to allow AJAX on TripalImporter forms once Dependency injection is used.
+   *
+   * The error message implies that the log exception this trait is needed to
+   * solve is caused by the form serializing an object that has an indirect
+   * reference to the database connection (TripalImporter) and that we should
+   * adjust your code so that is not necessary.
+   *
+   * That said, the TripalImporterForm does not appear to save the TripalImporter
+   * object in the form or form state at any point. Instead it only uses
+   * the importer object to get strings and arrays that are incorporated
+   * into the form.
+   *
+   * Anyway, using this trait solves the problem and although the error
+   * mentions this should be a temporary solution, there are no mentioned plans
+   * in the Drupal forumns or code that this trait will be removed at any point.
+   */
+  use DependencySerializationTrait;
+
   /**
    * The number of items that this importer needs to process. A progress
    * can be calculated by dividing the number of items process by this

tripal_chado/config/install/tripal.tripal_content_terms.chado_content_terms.yml

@@ -775,7 +775,9 @@ vocabularies:
             -   id: 'NCIT:C42699'
                 name: 'Namespace'
                 description: 'In general, a namespace is an abstract container, which is or could be filled by names, or technical terms, or words, and these represent or stand for real-world things. A description logic terminology namespace is a collection of Kind, Role, Property and Concept definitions. As in computer programming, context namespaces are intended to allow multiple knowledge bases to reside in the same physical database. (from Apelon) [ NCI ]'
-
+            -   id: 'NCIT:C70699'
+                name: 'Biospecimen'
+                description: 'Any material sample taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes, including a sample obtained from a living organism or taken from the biological object after halting of all its life functions.'
 
     -   name: 'ncbitaxon'
         label: 'NCBI organismal classification. An ontology representation of the NCBI organismal taxonomy'