Merge pull request #1641 from tripal/tv4g0-issue1389-typos

Tripal 4 Assorted typo fixes

tripal/src/Form/TripalImporterForm.php

@@ -128,7 +128,7 @@ public function buildForm(array $form, FormStateInterface $form_state, $plugin_i
     }
 
     // We should only add a submit button if this importer uses a button.
-    // Examples of importers who don't use this button are mutl-page forms.
+    // Examples of importers who don't use this button are multi-page forms.
     if (array_key_exists('use_button', $importer_def) AND $importer_def['use_button'] !== FALSE) {
       $form['button'] = [
         '#type' => 'submit',

tripal/src/Services/TripalFieldCollection.php

@@ -62,7 +62,7 @@ public static function create(ContainerInterface $container) {
    *
    * This function will only add defaults if the value is not already present
    * in the $field_def array. You can retrieve a fully populated definition
-   * array, with derfaults, by not passing an argument.  This function will
+   * array, with defaults, by not passing an argument.  This function will
    * remove any keys in the definition array that are not supported.
    *
    * @return array $field_def
@@ -201,7 +201,7 @@ public function setFieldDefDefaults(array $field_def = []) : array {
    * Validates a field definition array.
    *
    * This function can be used to check a field definition prior to adding
-   * the field to a Tripal content type..
+   * the field to a Tripal content type.
    *
    * @param array $field_def
    *   A definition array for the field.
@@ -321,7 +321,7 @@ public function install() {
    *     - storage_plugin_id: the name of the storage plugin
    *       (e.g. 'chado_storage').
    *     - storage_plugin_setings: an array of any settings that the storage
-   *       plugin expects for the field..
+   *       plugin expects for the field.
    *   - settings: (array) Any other settings needed for the field. Every
    *     field can have different settings.
    *   - display: Provides details for display of the field. By default it
@@ -413,7 +413,7 @@ public function addBundleField($field_def) : bool {
 
     try {
 
-      // Check if field storage exists for this field. If not, add it..
+      // Check if field storage exists for this field. If not, add it.
       $field_storage = FieldStorageConfig::loadByName('tripal_entity', $field_def['name']);
       if (!$field_storage) {
         $field_storage = FieldStorageConfig::create([

tripal/src/TripalDBX/TripalDbxSchema.php

@@ -744,7 +744,7 @@ public function foreignKeyConstraintExists(
    *   -'name': table name
    *   -'type': one of 'table', 'view', 'partition' and 'materialized view' for
    *     PostgreSQL materialized views.
-   *   -'status': either 'base' for base a table, or 'custom' for a custom table
+   *   -'status': either 'base' for a base table, or 'custom' for a custom table
    *     or a tripal materialized view, or 'other' for other elements.
    */
   public function getTables(

tripal/src/TripalStorage/StoragePropertyBase.php

@@ -63,7 +63,7 @@ public function __construct($entityType, $fieldType, $key, $term_id) {
       }
     }
     else {
-      throw new \Exception('Cannot create a StorageProperty object without a property formatted term: ' . $term_id);
+      throw new \Exception('Cannot create a StorageProperty object without a properly formatted term: ' . $term_id);
     }
 
     // Ensure we have required values.

tripal/src/TripalVocabTerms/TripalTerm.php

@@ -818,7 +818,7 @@ public function getInternalId() {
    * An array of synonyms.
    *
    * For easy lookup, this is an associative array where
-   * the key is the synonym and the value is the type term..
+   * the key is the synonym and the value is the type term.
    * Using the synonym as the key also prevents duplication.
    *
    * @var array

tripal/tests/src/Kernel/TripalImporter/TripalImporterBaseTest.php

@@ -140,9 +140,9 @@ public function testTripalImporterBase() {
       "The class should match our fake plugin name.");
     $selected_args = unserialize(base64_decode($records[0]->arguments));
     $this->assertIsArray($selected_args,
-      "Unable to retrieve arguements after creating tripal importer record.");
+      "Unable to retrieve arguments after creating tripal importer record.");
     $this->assertEquals($expected_args, $selected_args,
-      "We did not retreive the arguements we expected.");
+      "We did not retrieve the arguments we expected.");
 
     $importerTestLoad = $this->getMockForAbstractClass(
       '\Drupal\tripal\TripalImporter\TripalImporterBase',
@@ -151,9 +151,9 @@ public function testTripalImporterBase() {
     $importerTestLoad->load($import_id);
     $retrieved_args = $importerTestLoad->getArguments();
     $this->assertIsArray($retrieved_args,
-      "Unable to retrieve arguements after loading tripal importer.");
+      "Unable to retrieve arguments after loading tripal importer.");
     $this->assertEquals($expected_args, $retrieved_args,
-      "We did not retreive the arguements we expected after loading.");
+      "We did not retrieve the arguments we expected after loading.");
 
     // CASE --- Exception Expected
     // -- Empty run args, no file when file required.
@@ -214,9 +214,9 @@ public function testTripalImporterBase() {
       "The class should match our fake plugin name.");
     $selected_args = unserialize(base64_decode($records[0]->arguments));
     $this->assertIsArray($selected_args,
-      "Unable to retrieve arguements after creating tripal importer record.");
+      "Unable to retrieve arguments after creating tripal importer record.");
     $this->assertEquals($expected_args, $selected_args,
-      "We did not retreive the arguements we expected.");
+      "We did not retrieve the arguments we expected.");
 
     $importerTestLoad = $this->getMockForAbstractClass(
       '\Drupal\tripal\TripalImporter\TripalImporterBase',
@@ -225,9 +225,9 @@ public function testTripalImporterBase() {
     $importerTestLoad->load($import_id);
     $retrieved_args = $importerTestLoad->getArguments();
     $this->assertIsArray($retrieved_args,
-      "Unable to retrieve arguements after loading tripal importer.");
+      "Unable to retrieve arguments after loading tripal importer.");
     $this->assertEquals($expected_args, $retrieved_args,
-      "We did not retreive the arguements we expected after loading.");
+      "We did not retrieve the arguments we expected after loading.");
 
     // CASE --- Valid
     // -- run args + remote file.
@@ -262,9 +262,9 @@ public function testTripalImporterBase() {
       "The class should match our fake plugin name.");
     $selected_args = unserialize(base64_decode($records[0]->arguments));
     $this->assertIsArray($selected_args,
-      "Unable to retrieve arguements after creating tripal importer record.");
+      "Unable to retrieve arguments after creating tripal importer record.");
     $this->assertEquals($expected_args, $selected_args,
-      "We did not retreive the arguements we expected.");
+      "We did not retrieve the arguments we expected.");
 
     $importerTestLoad = $this->getMockForAbstractClass(
       '\Drupal\tripal\TripalImporter\TripalImporterBase',
@@ -273,9 +273,9 @@ public function testTripalImporterBase() {
     $importerTestLoad->load($import_id);
     $retrieved_args = $importerTestLoad->getArguments();
     $this->assertIsArray($retrieved_args,
-      "Unable to retrieve arguements after loading tripal importer.");
+      "Unable to retrieve arguments after loading tripal importer.");
     $this->assertEquals($expected_args, $retrieved_args,
-      "We did not retreive the arguements we expected after loading.");
+      "We did not retrieve the arguments we expected after loading.");
 
     // CASE --- Valid
     // -- run args + file upload (single file).
@@ -313,9 +313,9 @@ public function testTripalImporterBase() {
       "The class should match our fake plugin name.");
     $selected_args = unserialize(base64_decode($records[0]->arguments));
     $this->assertIsArray($selected_args,
-      "Unable to retrieve arguements after creating tripal importer record.");
+      "Unable to retrieve arguments after creating tripal importer record.");
     $this->assertEquals($expected_args, $selected_args,
-      "We did not retreive the arguements we expected.");
+      "We did not retrieve the arguments we expected.");
 
     $importerTestLoad = $this->getMockForAbstractClass(
       '\Drupal\tripal\TripalImporter\TripalImporterBase',
@@ -324,9 +324,9 @@ public function testTripalImporterBase() {
     $importerTestLoad->load($import_id);
     $retrieved_args = $importerTestLoad->getArguments();
     $this->assertIsArray($retrieved_args,
-      "Unable to retrieve arguements after loading tripal importer.");
+      "Unable to retrieve arguments after loading tripal importer.");
     $this->assertEquals($expected_args, $retrieved_args,
-      "We did not retreive the arguements we expected after loading.");
+      "We did not retrieve the arguments we expected after loading.");
 
     // CASE --- Valid
     // -- run args + file upload (multiple files).
@@ -367,9 +367,9 @@ public function testTripalImporterBase() {
       "The class should match our fake plugin name.");
     $selected_args = unserialize(base64_decode($records[0]->arguments));
     $this->assertIsArray($selected_args,
-      "Unable to retrieve arguements after creating tripal importer record.");
+      "Unable to retrieve arguments after creating tripal importer record.");
     $this->assertEquals($expected_args, $selected_args,
-      "We did not retreive the arguements we expected.");
+      "We did not retrieve the arguments we expected.");
 
     $importerTestLoad = $this->getMockForAbstractClass(
       '\Drupal\tripal\TripalImporter\TripalImporterBase',
@@ -378,9 +378,9 @@ public function testTripalImporterBase() {
     $importerTestLoad->load($import_id);
     $retrieved_args = $importerTestLoad->getArguments();
     $this->assertIsArray($retrieved_args,
-      "Unable to retrieve arguements after loading tripal importer.");
+      "Unable to retrieve arguments after loading tripal importer.");
     $this->assertEquals($expected_args, $retrieved_args,
-      "We did not retreive the arguements we expected after loading.");
+      "We did not retrieve the arguments we expected after loading.");
 
     // CASE --- Exception Expected
     // -- Load non-existant importer.
@@ -522,7 +522,7 @@ public function testTripalImporterBaseFiles() {
     $importer->prepareFiles();
     $retrieved_args = $importer->getArguments();
     $this->assertIsArray($retrieved_args,
-      "We could not retrieve arguements after preparing files");
+      "We could not retrieve arguments after preparing files");
     $this->assertArrayHasKey('file_path', $retrieved_args['files'][0],
       "The file_path should have been set during prepareFiles().");
 
@@ -549,7 +549,7 @@ public function testTripalImporterBaseFiles() {
     $importer->prepareFiles();
     $retrieved_args = $importer->getArguments();
     $this->assertIsArray($retrieved_args,
-      "We could not retrieve arguements after preparing files");
+      "We could not retrieve arguments after preparing files");
     $this->assertArrayHasKey('file_path', $retrieved_args['files'][0],
       "The file_path should have been set during prepareFiles().");
 

tripal/tests/src/Kernel/TripalImporter/TripalImporterFormBuildTest.php

@@ -163,7 +163,7 @@ public function testTripalImporterForm() {
 
     // Ensure we are able to build the form.
     $this->assertIsArray($form,
-      'We still expect the form builder to return a form array even without a plguin_id but it did not.');
+      'We still expect the form builder to return a form array even without a plugin_id but it did not.');
     $this->assertEquals('tripal_admin_form_tripalimporter', $form['#form_id'],
       'We did not get the form id we expected.');
 
@@ -245,7 +245,7 @@ public function testTripalImporterFormFiles() {
       $plugin_id,
     );
     $this->assertIsArray($form,
-      'We still expect the form builder to return a form array even without a plguin_id but it did not.');
+      'We still expect the form builder to return a form array even without a plugin_id but it did not.');
     $this->assertEquals('tripal_admin_form_tripalimporter', $form['#form_id'],
       'We did not get the form id we expected.');
 
@@ -299,7 +299,7 @@ public function testTripalImporterFormFiles() {
       $plugin_id,
     );
     $this->assertIsArray($form,
-      'We still expect the form builder to return a form array even without a plguin_id but it did not.');
+      'We still expect the form builder to return a form array even without a plugin_id but it did not.');
     $this->assertEquals('tripal_admin_form_tripalimporter', $form['#form_id'],
       'We did not get the form id we expected.');
 
@@ -334,7 +334,7 @@ public function testTripalImporterFormFiles() {
       $plugin_id,
     );
     $this->assertIsArray($form,
-      'We still expect the form builder to return a form array even without a plguin_id but it did not.');
+      'We still expect the form builder to return a form array even without a plugin_id but it did not.');
     $this->assertEquals('tripal_admin_form_tripalimporter', $form['#form_id'],
       'We did not get the form id we expected.');
 
@@ -369,7 +369,7 @@ public function testTripalImporterFormFiles() {
       $plugin_id,
     );
     $this->assertIsArray($form,
-      'We still expect the form builder to return a form array even without a plguin_id but it did not.');
+      'We still expect the form builder to return a form array even without a plugin_id but it did not.');
     $this->assertEquals('tripal_admin_form_tripalimporter', $form['#form_id'],
       'We did not get the form id we expected.');
 
@@ -414,7 +414,7 @@ public function testTripalImporterFormAnalysis() {
       $plugin_id,
     );
     $this->assertIsArray($form,
-      'We still expect the form builder to return a form array even without a plguin_id but it did not.');
+      'We still expect the form builder to return a form array even without a plugin_id but it did not.');
     $this->assertEquals('tripal_admin_form_tripalimporter', $form['#form_id'],
       'We did not get the form id we expected.');
 
@@ -448,7 +448,7 @@ public function testTripalImporterFormNoButton() {
       $plugin_id,
     );
     $this->assertIsArray($form,
-      'We still expect the form builder to return a form array even without a plguin_id but it did not.');
+      'We still expect the form builder to return a form array even without a plugin_id but it did not.');
     $this->assertEquals('tripal_admin_form_tripalimporter', $form['#form_id'],
       'We did not get the form id we expected.');
 

tripal/tests/src/Kernel/TripalStorage/PropertyBaseClassTest.php

@@ -96,7 +96,7 @@ public function testPropertyCreation() {
     catch (\Exception $e) {
       $exception_message = $e->getMessage();
     }
-    $this->assertStringContainsString('property formatted term', $exception_message,
+    $this->assertStringContainsString('properly formatted term', $exception_message,
       "We did not get the exception message we expected for passing in a badly formatted term.");
 
     // Test passing in a term whose ID Space doesn't exist in our mock.

tripal/tripal.views.inc

@@ -137,7 +137,7 @@ function tripal_views_data_jobs(&$data) {
 
   // Arguments
   $data['tripal_jobs']['arguments'] = [
-    'title' => t('Arguements'),
+    'title' => t('Arguments'),
     'help' => t('Any arguments passed to the callback.'),
     'field' => [
       'id' => 'standard',

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

@@ -221,7 +221,7 @@ vocabularies:
                 description: 'A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.'
             -   id: 'IAO:0000064'
                 name: 'algorithm'
-                description: 'An algorithm is a set of instructions for performing a paticular calculation.'
+                description: 'An algorithm is a set of instructions for performing a particular calculation.'
 
     -   name: 'null'
         label: 'No vocabulary'

tripal_chado/config/install/views.view.chado_mviews.yml

@@ -794,7 +794,7 @@ display:
           admin_label: ''
           plugin_id: text_custom
           empty: false
-          content: '<a class="button button-action button--primary button--small" href="[site:url]admin/tripal/storage/chado/mview">Add Materilaized View</a>'
+          content: '<a class="button button-action button--primary button--small" href="[site:url]admin/tripal/storage/chado/mview">Add Materialized View</a>'
           tokenize: false
       footer: {  }
       display_extenders: {  }

tripal_chado/src/Database/ChadoSchema.php

@@ -87,7 +87,7 @@ public function getSchemaDef(array $parameters) :array {
    *  include linker tables (which link two or more base tables), property
    * tables, and relationship tables.  These provide additional information
    * about primary data records and are therefore not base tables.  This
-   * function retreives only the list of tables that are considered 'base'
+   * function retrieves only the list of tables that are considered 'base'
    * tables.
    *
    * @return

tripal_chado/src/Plugin/Field/FieldWidget/ChadoContactWidgetDefault.php

@@ -39,7 +39,7 @@ public function formElement(FieldItemListInterface $items, $delta, array $elemen
     $results = $chado->query($sql, []);
 
     while ($contact = $results->fetchObject()) {
-      // Change the non-user-friendly 'null' contact, which is spedified by chado.
+      // Change the non-user-friendly 'null' contact, which is specified by chado.
       if ($contact->name == 'null') {
         $contact->name = '-- Unknown --';  // This will sort to the top.
       }

tripal_chado/src/Plugin/TripalIdSpace/ChadoIdSpace.php

@@ -984,7 +984,7 @@ public function setDescription($description) {
   }
 
   /**
-   * Retrieves from the Drupal cache the default vocabulary for this space..
+   * Retrieves from the Drupal cache the default vocabulary for this space.
    *
    * @return string
    *   The deffault vocabulary name.

tripal_chado/src/Plugin/TripalImporter/OBOImporter.php

@@ -2731,7 +2731,7 @@ private function insertChadoCvtermRelationship($subject_id, $type_id, $object_id
    *   The name of the vocabulary to add.
    *
    * @return object|NULL
-   *   The newly inserted CV object..
+   *   The newly inserted CV object.
    */
   private function insertChadoCv($cvname) {
     $chado = $this->getChadoConnection();

tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php

@@ -351,7 +351,7 @@ public function updateValues(&$values) : bool {
         }
       }
 
-      // Now insert all new values for nor the non-base table records.
+      // Now insert all new values for the non-base table records.
       foreach ($records as $chado_table => $deltas) {
         foreach ($deltas as $delta => $record) {
 
@@ -393,7 +393,7 @@ public function selectChadoRecord(&$records, $base_tables, $chado_table, $delta,
     }
 
     // If we are selecting on the base table and we don't have a proper
-    // condition then throw and error.
+    // condition then throw an error.
     if (!$this->hasValidConditions($record)) {
       throw new \Exception($this->t('Cannot select record in the Chado "@table" table due to unset conditions. Record: @record',
           ['@table' => $chado_table, '@record' => print_r($record, TRUE)]));
@@ -983,7 +983,7 @@ protected function addChadoRecordJoins(array &$records, string $chado_column, st
       ];
     }
 
-    // Get then current number of joins to the right table.
+    // Get the current number of joins to the right table.
     $num_left = 0;
     if (array_key_exists($left_table,$records[$parent_table][$delta]['joins'])) {
       $num_left = count($records[$parent_table][$delta]['joins'][$left_table]) - 1;

tripal_chado/src/Services/ChadoFieldDebugger.php

@@ -182,7 +182,7 @@ public function reportQuery(object $query, $message) {
      * We would like to complete print out the query with subbed in parameters
      * but it's driving me crazy.
      *
-     * Usually we would use $query->arguments() to get the arguements with
+     * Usually we would use $query->arguments() to get the arguments with
      * placeholders but there are a number of bugs here:
      *  - in Drupal 10 $insertQuery->arguments() provides a scope error.
      *  - $updateQuery->arguments() only provides the conditional arguments,