Merge branch '4.x' into g0.140-BringImporterShareToStandard

trpcultivate_phenotypes/src/Controller/TripalCultivatePhenotypesSettingsController.php

@@ -1,44 +1,70 @@
 <?php
 
-/**
- * @file
- * Controller to display a dashboard page that houses links and descriptions
- * to configuration pages.
- */
-
 namespace Drupal\trpcultivate_phenotypes\Controller;
 
 use Drupal\Core\Controller\ControllerBase;
-use Drupal\Core\Url;
+use Drupal\Core\Extension\ModuleHandlerInterface;
 use Drupal\Core\Link;
+use Drupal\Core\Url;
+use Symfony\Component\DependencyInjection\ContainerInterface;
 
 /**
  * Class definition TripalCultivatePhenotypesSettingsController.
+ *
+ * Controller to display a dashboard page that houses links and descriptions
+ * to configuration pages.
  */
 class TripalCultivatePhenotypesSettingsController extends ControllerBase {
 
   /**
-   * Returns a markup of details (fieldset) where the
-   * the title of the element is the configuration section and
-   * expanding each will reveal a short description.
+   * Module hander service.
+   *
+   * @var \Drupal\Core\Extension\ModuleHandlerInterface
+   */
+  protected $module_handler;
+
+  /**
+   * Constructor.
+   *
+   * @param \Drupal\Core\Extension\ModuleHandlerInterface $module_handler
+   *   The module handler service.
+   */
+  public function __construct(ModuleHandlerInterface $module_handler) {
+    $this->module_handler = $module_handler;
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function create(ContainerInterface $container) {
+    return new static(
+      $container->get('module_handler')
+    );
+  }
+
+  /**
+   * Provides an administrative list of phenotypes configuration pages.
+   *
+   * @return array
+   *   A render array consisting of a details element for each configuration
+   *   page where the title is the configuration section and the contents
+   *   include a short description plus a link.
    */
   public function loadPage() {
-    // Quick enabled or disabled status of sub-phenotypes modules
-    // and report to dashboard.
-    $moduleHandler = \Drupal::service('module_handler');
+    // Quick enabled or disabled status of sub-phenotypes modules and report
+    // to dashboard.
     $status_message = 'Tripal Cultivate Phenotypes Modules Status: ';
 
-    foreach(['trpcultivate_phenoshare', 'trpcultivate_phenocollect'] as $m) {
-      $is_enabled = ($moduleHandler->moduleExists($m)) ? 'is enabled' : 'is disabled';
+    foreach (['trpcultivate_phenoshare', 'trpcultivate_phenocollect'] as $m) {
+      $is_enabled = ($this->module_handler->moduleExists($m)) ? 'is enabled' : 'is disabled';
       $status_message .= '*' . $m . ' ' . $is_enabled . ' ';
     }
 
     $url = Url::fromUri('internal:/admin/modules');
     $link = Link::fromTextAndUrl('Manage Modules', $url)
       ->toString();
 
-    $this->messenger()->addStatus($this->t($status_message . '- @manage', ['@manage' => $link]));
-
+    $this->messenger()->addStatus($status_message . ' - ' . $link);
 
     // Describe R Rules configuration:
     $url = Url::fromRoute('trpcultivate_phenotypes.settings_r');
@@ -90,4 +116,5 @@ public function loadPage() {
 
     return $element;
   }
-}
+
+}

trpcultivate_phenotypes/src/Form/TripalCultivatePhenotypesOntologySettingsForm.php

@@ -148,10 +148,14 @@ public function buildForm(array $form, FormStateInterface $form_state) {
         $link_to_docs = Link::fromTextAndUrl($this->t('Tripal 4 User Guide'), $url)
           ->toString();
 
+        $placeholder_values = [
+          '@tripaljobs' => $link_to_jobs,
+          '@tripaldocs' => $link_to_docs,
+        ];
         $config_warning = $this->t('Tripal Cultivate Phenotypes module requires controlled vocabulary terms and genus records
           used for creating terms and genus-ontology module configuration. If you already know how to execute a Tripal Job,
           please proceed with the Tripal Job Id number for Tripal Job titled: Tripal Cultivate Phenotypes: Install Ontology and Terms
-          (@tripaljobs), otherwise, please visit @tripaldocs to learn more about Tripal Jobs.', ['@tripaljobs' => $link_to_jobs, '@tripaldocs' => $link_to_docs]);
+          (@tripaljobs), otherwise, please visit @tripaldocs to learn more about Tripal Jobs.', $placeholder_values);
 
         $this->messenger()->addWarning($config_warning);
         return $form;
@@ -325,9 +329,9 @@ public function buildForm(array $form, FormStateInterface $form_state) {
     // Render each term as autocomplete field element.
     foreach ($this->config_vars['terms'] as $config => $prop) {
       // Field description.
-      $describe = $this->t($prop['help_text']);
+      $describe = $prop['help_text'];
       // Field placeholder and title text.
-      $placeholder = $title = $this->t(ucwords($prop['name']));
+      $placeholder = $title = ucwords($prop['name']);
       // Field default value.
       $config_value = $this->service_terms->getTermId($config);
       $default_value = ChadoCVTermAutocompleteController::formatCVterm($config_value);

trpcultivate_phenotypes/src/Form/TripalCultivatePhenotypesRSettingsForm.php

@@ -1,21 +1,18 @@
 <?php
 
-/**
- * @file
- * Construct form to manage and configure R Transformation rules.
- */
-
 namespace Drupal\trpcultivate_phenotypes\Form;
 
 use Drupal\Core\Form\ConfigFormBase;
 use Drupal\Core\Form\FormStateInterface;
 
 /**
  * Class definition TripalCultivatePhenotypesRSettingsForm.
+ *
+ * Construct form to manage and configure R Transformation rules.
  */
 class TripalCultivatePhenotypesRSettingsForm extends ConfigFormBase {
   const SETTINGS = 'trpcultivate_phenotypes.settings';
-  
+
   /**
    * {@inheritdoc}
    */
@@ -30,26 +27,26 @@ protected function getEditableConfigNames() {
     return [
       static::SETTINGS,
     ];
-  }  
-  
-  /** 
+  }
+
+  /**
    * {@inheritdoc}
    */
   public function buildForm(array $form, FormStateInterface $form_state) {
     $config = $this->config(static::SETTINGS);
     $config_r = 'trpcultivate.phenotypes.r_config.';
-    
+
     $form['description'] = [
       '#markup' => $this->t('Tripal Cultivate Phenotypes supports R language for statistical computing by providing
-      syntactically valid version of trait or values. Use R Transformation Rules configuration page to define 
-      standard transformation rules to apply to trait or string when converting to R version.')
+      syntactically valid version of trait or values. Use R Transformation Rules configuration page to define
+      standard transformation rules to apply to trait or string when converting to R version.'),
     ];
 
     $form['words'] = [
       '#type' => 'textarea',
       '#title' => $this->t('List of words to remove'),
       '#default_value' => implode(',', $config->get($config_r . 'words')),
-      '#description' => $this->t('Separate each word entry with a comma character. 
+      '#description' => $this->t('Separate each word entry with a comma character.
         Words must at least be 2 characters or more.'),
       '#required' => TRUE,
     ];
@@ -58,7 +55,7 @@ public function buildForm(array $form, FormStateInterface $form_state) {
       '#type' => 'textarea',
       '#title' => $this->t('List of special characters to remove'),
       '#default_value' => implode(',', $config->get($config_r . 'chars')),
-      '#description' => $this->t('Separate each character entry with a comma character. 
+      '#description' => $this->t('Separate each character entry with a comma character.
         Characters must be 1 character only.'),
       '#required' => TRUE,
     ];
@@ -67,12 +64,11 @@ public function buildForm(array $form, FormStateInterface $form_state) {
       '#type' => 'textarea',
       '#title' => $this->t('Match word and replace with'),
       '#default_value' => implode(',', $config->get($config_r . 'replace')),
-      '#description' => $this->t('Separate match and replace pairs with a comma character. 
+      '#description' => $this->t('Separate match and replace pairs with a comma character.
         Use match = replace pattern for each combination.'),
       '#required' => TRUE,
     ];
-
-
+
     return parent::buildForm($form, $form_state);
   }
 
@@ -82,33 +78,33 @@ public function buildForm(array $form, FormStateInterface $form_state) {
   public function validateForm(array &$form, FormStateInterface $form_state) {
     // Words: words must be at least 2 characters long.
     if ($words = $form_state->getValue('words')) {
-      foreach(explode(',', $words) as $word) {
+      foreach (explode(',', $words) as $word) {
         if (empty($word) || !preg_match('/\w{2,}/', $word)) {
           $form_state->setErrorByName('word', $this->t('Could not save rule.
             Empty or invalid word: @word added to the list.', ['@word' => $word]));
         }
       }
     }
-    
+
     // Special characters: 1 character only, excluding comma symbol since
     // it is used as delimiter.
     if ($chars = $form_state->getValue('chars')) {
-      foreach(explode(',', $chars) as $char) {
+      foreach (explode(',', $chars) as $char) {
         if (empty($char) || $char == ',' || !preg_match('/\W{1}/', $char)) {
           $form_state->setErrorByName('chars', $this->t('Could not save rule.
-            Empty or invalid special characters: @char added to the list.', ['@char' => $char]));        
+            Empty or invalid special characters: @char added to the list.', ['@char' => $char]));
         }
       }
     }
 
     // Match and replace: match = replace pattern, excluding comma symbol since
     // it is used as delimiter.
     if ($replaces = $form_state->getValue('replace')) {
-      foreach(explode(',', $replaces) as $replace) {
+      foreach (explode(',', $replaces) as $replace) {
         if (empty($replace) || !preg_match('/^[^,]+\s{1}[=]\s{1}[^,]+$/', $replace)) {
-          $form_state->setErrorByName('replace', $this->t('Could not save rule. 
-            Empty or invalid match and replace: @replace added to the list.', ['@replace' => $replace]));        
-        }  
+          $form_state->setErrorByName('replace', $this->t('Could not save rule.
+            Empty or invalid match and replace: @replace added to the list.', ['@replace' => $replace]));
+        }
       }
     }
   }
@@ -118,8 +114,8 @@ public function validateForm(array &$form, FormStateInterface $form_state) {
    */
   public function submitForm(array &$form, FormStateInterface $form_state) {
     $config_r = 'trpcultivate.phenotypes.r_config.';
-    
-    // Configuration in field are string, convert to array to match 
+
+    // Configuration in field are string, convert to array to match
     // configuration schema data type.
     $this->configFactory->getEditable(static::SETTINGS)
       ->set($config_r . 'words', explode(',', $form_state->getValue('words')))
@@ -129,4 +125,5 @@ public function submitForm(array &$form, FormStateInterface $form_state) {
 
     return parent::submitForm($form, $form_state);
   }
-}
+
+}