Merge pull request #1390 from tripal/tv4g0-issue1389-typos

Tv4g0 issue1389 typos

tripal/config/schema/tripal.schema.yml

@@ -21,15 +21,15 @@ tripal.tripal_content_terms.*:
         mapping:
           name:
             type: string
-            label: 'Vocbulary Name'
+            label: 'Vocabulary Name'
             nullable: false
           label:
             type: string
-            label: 'Vocbulary Label'
+            label: 'Vocabulary Label'
             nullable: false
           url:
             type: string
-            label: 'Vocbulary URL'
+            label: 'Vocabulary URL'
             nullable: false
           idSpaces:
             type: sequence

tripal/js/tripal.js

@@ -107,7 +107,7 @@
     this.id = id;
     this.hide_empty_field = hide_empty_field;
 
-    // Get the pane that this field beongs to (if one exists).
+    // Get the pane that this field belongs to (if one exists).
     this.pane = this.getPane(); 
   }
 

tripal/js/tripal.user_files.js

@@ -63,7 +63,7 @@
   }
 
   /**
-   * Expands a node in the CV tree browser and loads it's children via AJAX.
+   * Expands a node in the CV tree browser and loads its children via AJAX.
    */
   function expandNode(item){
     item.removeClass('tree-node-closed');

tripal/src/Entity/TripalEntity.php

@@ -459,9 +459,9 @@ public static function baseFieldDefinitions(EntityTypeInterface $entity_type) {
   }
 
   /**
-   * Retruns an associative array of property type value for the enitty.
+   * Returns an associative array of property type value for the entity.
    *
-   * The array is keyed in the following leveles:
+   * The array is keyed in the following levels:
    * - 1st: Tripal Stroage Plugin ID
    * - 2nd: Field name
    * - 3rd: Delta value of the field item.
@@ -685,7 +685,7 @@ public static function postLoad(EntityStorageInterface $storage, array &$entitie
           $delta = $item->getName();
           $tsid = $item->tripalStorageId();
 
-          // reate a new properties array for this field item.
+          // Create a new properties array for this field item.
           $prop_values = [];
           $prop_types = [];
           foreach ($values[$tsid][$field_name][$delta] as $key => $info) {
@@ -704,7 +704,7 @@ public static function postLoad(EntityStorageInterface $storage, array &$entitie
    * {@inheritdoc}
    */
   public function validate() {
-    // Let the parent class do it's validations and return the violoations list.
+    // Let the parent class do its validations and return the violations list.
     $violations = parent::validate();
 
     // Create a values array appropriate for `loadValues()`

tripal/src/Entity/TripalEntityStorageSchema.php

@@ -20,7 +20,7 @@ public function onFieldableEntityTypeCreate(EntityTypeInterface $entity_type, ar
     foreach ($field_storage_definitions as $storageDefinition) {
       $field = \Drupal::service("plugin.manager.field.field_type").getInstance($storageDefinition->getType());
       if ($field instanceof TripalFieldItemInterface) {
-        // Each field can define it's value as a single-depth array of
+        // Each field can define its value as a single-depth array of
         // key => value pairs where the key is a name for that data (e.g. accession )
         // and the value is an implementation of StoragePropertyTypeBase setting the
         // type of the value (e.g. string).
@@ -31,7 +31,7 @@ public function onFieldableEntityTypeCreate(EntityTypeInterface $entity_type, ar
         // Note: this can be changed in the admin UI since all TripalStorage
         // types are expected to be able to read this key-value structure.
         $tsid = $field->tripalStorageId();
-        // Since each StoragePropertyTypeBase implementation knows it's
+        // Since each StoragePropertyTypeBase implementation knows its
         // key (saved as id) and associated field, we can merge them all here
         // without saving the key mapping.
         // We're basically just compiling all field property types with the
@@ -132,7 +132,7 @@ public function onFieldableEntityTypeUpdate(EntityTypeInterface $entity_type, En
           }
         }
         // Case 2: the new field did not exist before.
-        //   - we will need to add the new field to it's new storage.
+        //   - we will need to add the new field to its new storage.
         else {
           if (array_key_exists($tsid, $storageAdd)) {
             $storageAdd[$tsid] = array_merge($storageAdd[$tsid], $types);

tripal/src/Entity/TripalEntityType.php

@@ -187,7 +187,7 @@ public static function create(array $values = []) {
 
     // Let the parent implementation finish creating the object.
     // NOTE: We do things in this order because a configuration entity cannot
-    // save an object to it's storage. Thus we need to extract the term strings
+    // save an object to its storage. Thus we need to extract the term strings
     // for storage and retrieve the Term object later if requested via getTerm().
     return parent::create($values);
   }

tripal/src/Form/Register.php

@@ -323,7 +323,7 @@ public function submitForm(array &$form, FormStateInterface $form_state) {
     \Drupal::state()->set('tripal_site_registration', $form_state);
 
     // Now send the updated info to the Tripal Site.
-    // Only register with tripal.info if the user has not opt'd out.
+    // Only register with tripal.info if the user has not opted out.
     $messenger = \Drupal::messenger();
     if ($form_state->getValue('disable_tripal_reporting') == FALSE) {
       $this->tripal_registration_remote_submit($form_state);

tripal/src/Form/TripalAdminAddCustomForm.php

@@ -125,7 +125,7 @@ public function submitForm(array &$form, FormStateInterface $form_state) {
     $quota = $form_state->getValue('quota');
     $expiration = $form_state->getValue('expiration');
 
-    // if the 2nd element of the qutoa string occupied by a valid suffix we need to check to see
+    // if the 2nd element of the quota string occupied by a valid suffix we need to check to see
     // what we have to multiply the value by (1024 for GB 1024^2 for TB because
     // we assume that the initial number is already in MB)
     $matches = [];

tripal/src/Form/TripalAdminManageFilesForm.php

@@ -80,7 +80,7 @@ public function validateForm(array &$form, FormStateInterface $form_state) {
   public function submitForm(array &$form, FormStateInterface $form_state) {
     $upload_max = $form_state->getValue('upload_max');
 
-    // if the 2nd element of the qutoa string occupied by a valid suffix we need to check to see
+    // if the 2nd element of the quota string occupied by a valid suffix we need to check to see
     // what we have to multiply the value by (1024 for GB 1024^2 for TB because
     // we assume that the initial number is already in MB)
     $matches = [];

tripal/src/Form/TripalAdminManageQuotaForm.php

@@ -124,7 +124,7 @@ public function submitForm(array &$form, FormStateInterface $form_state) {
     $quota = $form_state->getValue('quota');
     $expiration = $form_state->getValue('expiration');
 
-    // if the 2nd element of the qutoa string occupied by a valid suffix we need to check to see
+    // if the 2nd element of the quota string occupied by a valid suffix we need to check to see
     // what we have to multiply the value by (1024 for GB 1024^2 for TB because
     // we assume that the initial number is already in MB)
     $matches = [];

tripal/src/Form/TripalEntityTypeForm.php

@@ -48,7 +48,7 @@ public function form(array $form, FormStateInterface $form_state) {
     // As mentioned above, the term cannot be changed later!
     // As such, if this is not a new content type then we will only take into
     // account the set term (not the form state) and disable the field.
-    // NOTE: we go this route because only showin the field on the add page
+    // NOTE: we go this route because only showing the field on the add page
     // causes a validation error.
     else {
       $vocab_label = $term_name = $term_accession = '';

tripal/src/Form/TripalFileQuota.php

@@ -179,7 +179,7 @@ public function submitForm(array &$form, FormStateInterface $form_state) {
     $quota = $form_state->getValue('default_quota');
     $expiration = $form_state->getValue('default_expiration_date');
 
-    // if the 2nd element of the qutoa string occupied by a valid suffix we need to check to see
+    // if the 2nd element of the quota string occupied by a valid suffix we need to check to see
     // what we have to multiply the value by (1024 for GB 1024^2 for TB because
     // we assume that the initial number is already in MB)
     $matches = [];

tripal/src/Form/TripalFileQuotaCustomEdit.php

@@ -116,7 +116,7 @@ public function submitForm(array &$form, FormStateInterface $form_state) {
     $quota = $form_state->getValue('quota');
     $expiration = $form_state->getValue('expiration');
 
-    // if the 2nd element of the qutoa string occupied by a valid suffix we need to check to see
+    // if the 2nd element of the quota string occupied by a valid suffix we need to check to see
     // what we have to multiply the value by (1024 for GB 1024^2 for TB because
     // we assume that the initial number is already in MB)
     $matches = [];

tripal/src/Form/TripalImporterForm.php

@@ -265,7 +265,7 @@ public function validateForm(array &$form, FormStateInterface $form_state) {
       $form_state->setErrorByName('file_local', t("You must provide a file."));
     }
 
-    // Now allow the loader to do validation of it's form additions.
+    // Now allow the loader to do validation of its form additions.
     $importer->formValidate($form, $form_state);
   }
 }

tripal/src/Services/TripalFieldsManager.php

@@ -135,7 +135,7 @@ public function setFieldDefDefaults(array $field_def = []) : array {
       foreach ($field_def['display'] as $display_type => $view_modes) {
         foreach ($view_modes as  $view_mode => $mode_config) {
           foreach ($mode_config as $setting_name => $value) {
-            // Maake sure the label is an allowed value.
+            // Make sure the label is an allowed value.
             if ($setting_name == 'label') {
               if (in_array($value, ['above', 'inline', 'hidden', 'visually_hidden'])) {
                 $new_defs['display'][$display_type][$view_mode][$setting_name] = $value;

tripal/src/TripalDBX/TripalDbxConnection.php

@@ -348,7 +348,7 @@ public function __construct(
     // Check if a Tripal DBX managed schema name has been specified.
     if (!empty($schema_name)) {
       // We must use this PostgreSQL schema instead of the Drupal one as default
-      // for this dtaabase connection. To do so, we use the schema name as a
+      // for this database connection. To do so, we use the schema name as a
       // prefix (which is supported by Drupal PostgreSQL implementation).
       // If there are table-specific prefixes set, we assume the user knows what
       // he/she wants to do and we won't change those.
@@ -1253,7 +1253,7 @@ public function executeSqlQueries(
         foreach ($search_path_mode as $old_name => $replacement) {
 
           // Ensure the replacement pattern is sanitized.
-          // Secure replacement (we allow comas and spaces).
+          // Secure replacement (we allow commas and spaces).
           $replacement = preg_replace(
             '/[^a-z_\\xA0-\\xFF0-9\s,]+/',
             '',

tripal/src/TripalDBX/TripalDbxSchema.php

@@ -9,7 +9,7 @@
 /**
  * Tripal DBX API Schema class.
  *
- * NOTE: This class should not be instanciated directly but rather it should
+ * NOTE: This class should not be instantiated directly but rather it should
  * be accessed through a TripalDbxConnection object using the schema() method.
  *
  * This class provides a Tripal-specific implementation of the Drupal Schema
@@ -106,14 +106,14 @@ abstract public function getSchemaDef(array $parameters) :array;
    *
    * Overrides default constructor to manage the Tripal DBX managed schema name.
    *
-   * The TripalDbxSchema object should be instanciated by the
+   * The TripalDbxSchema object should be instantiated by the
    * TripalDbxConnection::schema() method in order to avoid issues when the
    * default Tripal DBX managed schema name is changed in the TripalDbxConnection
    * object which could lead to issues.
    *
-   * If you choose to instanciate a TripalDbxSchema object yourself, you are
+   * If you choose to instantiate a TripalDbxSchema object yourself, you are
    * responsible to not change the Tripal DBX managed schema name of the connection
-   * object used to instanciate this TripalDbxSchema.
+   * object used to instantiate this TripalDbxSchema.
    *
    * @param \Drupal\tripal\TripalDBX\TripalDbxConnection $connection
    *   A Tripal DBX connection object.
@@ -747,7 +747,7 @@ public function getTables(
     ;
 
     $tables = [];
-    // Get original schema to differenciate base and custom.
+    // Get original schema to differentiate base and custom.
     $schema_def = $this->getSchemaDef(['source' => 'file']);
 
     // Check if tables should be filtered according to their origin

tripal/src/TripalStorage/Interfaces/TripalStorageInterface.php

@@ -50,7 +50,7 @@ public function getTypes();
    *   - "value": a \Drupal\tripal\TripalStorage\StoragePropertyValue object
    *   - "type": a\Drupal\tripal\TripalStorage\StoragePropertyType object
    *   - "definition": a \Drupal\Field\Entity\FieldConfig object
-   *   When the function returns, any values retreived from the data store
+   *   When the function returns, any values retrieved from the data store
    *   will be set in the StoragePropertyValue object.
    *
    * @return bool
@@ -70,7 +70,7 @@ public function insertValues(&$values) : bool;
    *   - "value": a \Drupal\tripal\TripalStorage\StoragePropertyValue object
    *   - "type": a\Drupal\tripal\TripalStorage\StoragePropertyType object
    *   - "definition": a \Drupal\Field\Entity\FieldConfig object
-   *   When the function returns, any values retreived from the data store
+   *   When the function returns, any values retrieved from the data store
    *   will be set in the StoragePropertyValue object.
    *
    * @return bool

tripal/src/TripalStorage/TripalEntityBase.php

@@ -102,7 +102,7 @@ public static function postLoad(EntityStorageInterface $storage, array &$entitie
 
     // Add loaded properties to their correct entity and field references
     // Note: Each $property is an instance of StoragePropertyValue
-    // and thus contains information for it's associated entity ID/Type and
+    // and thus contains information for its associated entity ID/Type and
     // field ID/Key.
     foreach ($loaded as $property) {
       $tid = $property->getEntityId();
@@ -121,8 +121,8 @@ public static function postLoad(EntityStorageInterface $storage, array &$entitie
       $entity = $entityRef["entity"];
       foreach ($entityRef as $fieldRef) {
         $field = $fieldRef["field"];
-        // Finally we let the TripalField attach the it's loaded properties
-        // which allows another opprotunity for re-organization if needed.
+        // Finally we let the TripalField attach its loaded properties
+        // which allows another opportunity for re-organization if needed.
         $field->tripalLoad($fieldRef["props"],$entity);
       }
     }

tripal/src/api/tripal.importer.api.php

@@ -57,7 +57,7 @@ function hook_importer_start($importer) {
 /**
  * Implements hook_importer_finish().
  *
- * This hook is executed once a TripalImporter has completed but it's run
+ * This hook is executed once a TripalImporter has completed both its run
  * and post run activities.  This allows modules to implement specific actions
  * once loaders are completed.
  *
@@ -138,7 +138,7 @@ function tripal_run_importer($import_id, TripalJob $job = NULL) {
       $function($importer);
     }
 
-    // @todo uncooment the section below once these functions are available.
+    // @todo uncomment the section below once these functions are available.
 
     // Check for tables with new cvterms
 //     $logger->notice("Remapping Chado Controlled vocabularies to Tripal Terms...");
@@ -213,4 +213,4 @@ function tripal_run_importer_post_run($loader, $logger) {
     $transaction->rollback();
     throw $e;
   }
-}
+}

tripal/tests/src/Functional/Entity/EntityAccessTest.php

@@ -43,7 +43,7 @@ public function testTripalAccessOwnContentCheck() {
   public function testTripalEntityAccessControlHandler() {
 
     // One user per permission to check.
-    $user_unpriviledged = $this->drupalCreateUser([]);
+    $user_unprivileged = $this->drupalCreateUser([]);
     $user_view = $this->drupalCreateUser(['view tripal content entities']);
     $user_edit = $this->drupalCreateUser(['edit tripal content entities']);
     $user_delete = $this->drupalCreateUser(['delete tripal content entities']);
@@ -74,8 +74,8 @@ public function testTripalEntityAccessControlHandler() {
     $entity_type_interface = \Drupal::entityTypeManager()->getDefinition('tripal_entity');
     $access_check_obj = new \Drupal\Tests\tripal\Functional\Entity\Subclass\TripalEntityAccessControlHandlerFake($entity_type_interface);
 
-    $result = $access_check_obj->returnProtectedCheckAccess($entity, 'view', $user_unpriviledged);
-    $this->assertInstanceOf(AccessResultNeutral::class, $result, "An unpriviledged user should NOT be allowed to VIEW the entity.");
+    $result = $access_check_obj->returnProtectedCheckAccess($entity, 'view', $user_unprivileged);
+    $this->assertInstanceOf(AccessResultNeutral::class, $result, "An unprivileged user should NOT be allowed to VIEW the entity.");
     $result = $access_check_obj->returnProtectedCheckAccess($entity, 'view', $user_view);
     $this->assertInstanceOf(AccessResultAllowed::class, $result, "A user with view permission should be allowed to VIEW the entity.");
     $result = $access_check_obj->returnProtectedCheckAccess($entity, 'view', $user_edit);
@@ -85,8 +85,8 @@ public function testTripalEntityAccessControlHandler() {
     $result = $access_check_obj->returnProtectedCheckAccess($entity, 'view', $user_add);
     $this->assertInstanceOf(AccessResultNeutral::class, $result, "A user with add permission should NOT be allowed to VIEW the entity.");
 
-    $result = $access_check_obj->returnProtectedCheckAccess($entity, 'update', $user_unpriviledged);
-    $this->assertInstanceOf(AccessResultNeutral::class, $result, "An unpriviledged user should NOT be allowed to UPDATE the entity.");
+    $result = $access_check_obj->returnProtectedCheckAccess($entity, 'update', $user_unprivileged);
+    $this->assertInstanceOf(AccessResultNeutral::class, $result, "An unprivileged user should NOT be allowed to UPDATE the entity.");
     $result = $access_check_obj->returnProtectedCheckAccess($entity, 'update', $user_view);
     $this->assertInstanceOf(AccessResultNeutral::class, $result, "A user with view permission should NOT be allowed to UPDATE the entity.");
     $result = $access_check_obj->returnProtectedCheckAccess($entity, 'update', $user_edit);
@@ -96,8 +96,8 @@ public function testTripalEntityAccessControlHandler() {
     $result = $access_check_obj->returnProtectedCheckAccess($entity, 'update', $user_add);
     $this->assertInstanceOf(AccessResultNeutral::class, $result, "A user with add permission should NOT be allowed to UPDATE the entity.");
 
-    $result = $access_check_obj->returnProtectedCheckAccess($entity, 'delete', $user_unpriviledged);
-    $this->assertInstanceOf(AccessResultNeutral::class, $result, "An unpriviledged user should NOT be allowed to DELETE the entity.");
+    $result = $access_check_obj->returnProtectedCheckAccess($entity, 'delete', $user_unprivileged);
+    $this->assertInstanceOf(AccessResultNeutral::class, $result, "An unprivileged user should NOT be allowed to DELETE the entity.");
     $result = $access_check_obj->returnProtectedCheckAccess($entity, 'delete', $user_view);
     $this->assertInstanceOf(AccessResultNeutral::class, $result, "A user with view permission should be allowed to DELETE the entity.");
     $result = $access_check_obj->returnProtectedCheckAccess($entity, 'delete', $user_edit);
@@ -107,8 +107,8 @@ public function testTripalEntityAccessControlHandler() {
     $result = $access_check_obj->returnProtectedCheckAccess($entity, 'delete', $user_add);
     $this->assertInstanceOf(AccessResultNeutral::class, $result, "A user with add permission should NOT be allowed to DELETE the entity.");
 
-    $result = $access_check_obj->returnProtectedCheckCreateAccess($user_unpriviledged);
-    $this->assertInstanceOf(AccessResultNeutral::class, $result, "An unpriviledged user should NOT be allowed to CREATE the entity.");
+    $result = $access_check_obj->returnProtectedCheckCreateAccess($user_unprivileged);
+    $this->assertInstanceOf(AccessResultNeutral::class, $result, "An unprivileged user should NOT be allowed to CREATE the entity.");
     $result = $access_check_obj->returnProtectedCheckCreateAccess($user_view);
     $this->assertInstanceOf(AccessResultNeutral::class, $result, "A user with view permission should NOT be allowed to CREATE the entity.");
     $result = $access_check_obj->returnProtectedCheckCreateAccess($user_edit);