Automated Field Testing: focused on the field creation forms in Drupal 10.2+

tripal/config/schema/tripal_entity_type.schema.yml

@@ -32,3 +32,9 @@ tripal.content_type.*:
  ajax_field:
  type: boolean
  label: 'AJAX Field Loading'
+ third_party_settings:
+ type: mapping
+ mapping:
+ tripal:
+ type: mapping
+ label: "Tripal Third-party settings"

tripal/src/TripalVocabTerms/TripalIdSpaceBase.php

@@ -21,16 +21,18 @@ public function __construct(array $configuration, $plugin_id, $plugin_definition
  * {@inheritdoc}
  */
  public function setDefaultVocabulary($name) {
- 
+
  if (!is_string($name)) {
  return False;
- } 
- 
+ }
+
  $manager = \Drupal::service('tripal.collection_plugin_manager.vocabulary');
  $oldname = $this->getDefaultVocabulary();
  if ($oldname) {
  $vocab = $manager->loadCollection($oldname);
- $vocab->removeIdSpace($this->getName());
+ if ($vocab) {
+ $vocab->removeIdSpace($this->getName());
+ }
  }
  if ($name) {
  $vocab = $manager->loadCollection($name);

tripal_chado/tests/src/Functional/Plugin/Fields/CreateEditFieldForms/BasicDataTypeChadoFieldTest.php

@@ -0,0 +1,267 @@
+<?php
+
+namespace Drupal\Tests\tripal_chado\Functional\Plugin\Fields\CreateEditFieldForms;
+
+use Drupal\Tests\field_ui\Traits\FieldUiTestTrait;
+use Drupal\Tests\tripal_chado\Functional\ChadoTestBrowserBase;
+
+/**
+ * Tests the configuration for where a basic chado field is added to an existing
+ * content type. Specific field types tested are below in the $field_types
+ * property --these are fields that act on individual columns in the base table
+ * and require their column to be set in the field storage settings.
+ *
+ * @group ChadoField
+ */
+class BasicDataTypeChadoFieldTest extends ChadoTestBrowserBase {
+ use FieldUiTestTrait;
+
+ protected $defaultTheme = 'stark';
+
+ protected static $modules = ['system', 'user', 'field_ui', 'tripal', 'tripal_chado'];
+
+ /**
+ * Provides a list of the field types we are testing with this class.
+ */
+ protected static array $field_types = [
+ 'chado_integer_type_default',
+ 'chado_boolean_type_default',
+ 'chado_string_type_default',
+ 'chado_text_type_default',
+ ];
+
+ /**
+ * The machine name of the Tripal Content Type used by tests in this class.
+ */
+ protected $type = 'gene';
+
+ protected $connection;
+
+ /**
+ * {@inheritdoc}
+ */
+ protected function setUp() : void {
+ parent::setUp();
+
+ // Installs up the chado with all the items added via the prepare.
+ // NOTE: This done not prepare Drupal so none of the TripalTerms we need are available.
+ $this->connection = $this->getTestSchema(ChadoTestBrowserBase::PREPARE_TEST_CHADO);
+
+ // Create the Organism Content Type
+ $content_type = $this->createTripalContentType([
+ 'label' => 'Gene',
+ 'termIdSpace' => 'SO',
+ 'termAccession' => '0000704',
+ 'category' => 'Genomic',
+ 'id' => $this->type,
+ 'help_text' => 'Use the gene page for a region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.',
+ ]);
+ $content_type->setThirdPartySetting('tripal', 'chado_base_table', 'feature');
+ $content_type->save();
+
+ // Create test user.
+ $admin_user = $this->drupalCreateUser([
+ 'access content',
+ 'administer tripal',
+ 'manage tripal content types',
+ 'administer tripal_entity fields',
+ ]);
+ $this->drupalLogin($admin_user);
+
+ // Create the Tripal Terms we need.
+ // -- SIO:000729
+ $this->createTripalTerm([
+ 'vocab_name' => 'SIO',
+ 'id_space_name' => 'SIO',
+ 'term' => [
+ 'name' => 'record identifier',
+ 'definition' => 'A record identifier is an identifier for a database entry.',
+ 'accession' =>'000729',
+ ]],
+ 'chado_id_space', 'chado_vocabulary'
+ );
+ $this->createTripalTerm([
+ 'vocab_name' => 'SO',
+ 'id_space_name' => 'SO',
+ 'term' => [
+ 'name' => 'sequence_feature',
+ 'definition' => 'Any extent of continuous biological sequence.',
+ 'accession' => '0000110',
+ ]
+ ],
+ 'chado_id_space',
+ 'chado_vocabulary'
+ );
+ $this->createTripalTerm([
+ 'vocab_name' => 'local',
+ 'id_space_name' => 'local',
+ 'term' => [
+ 'name' => 'is_analysis',
+ 'accession' => 'is_analysis',
+ ]
+ ],
+ 'chado_id_space',
+ 'chado_vocabulary'
+ );
+ $this->createTripalTerm([
+ 'vocab_name' => 'schema',
+ 'id_space_name' => 'schema',
+ 'term' => [
+ 'name' => 'name',
+ 'accession' => 'name',
+ ]
+ ],
+ 'chado_id_space',
+ 'chado_vocabulary'
+ );
+ $this->createTripalTerm([
+ 'vocab_name' => 'edam',
+ 'id_space_name' => 'data',
+ 'term' => [
+ 'name' => 'Identifier',
+ 'accession' => '0842',
+ ]
+ ],
+ 'chado_id_space',
+ 'chado_vocabulary'
+ );
+ }
+
+ /**
+ * Data Provider: provides a list of the basic fields to test.
+ */
+ public function provideFieldsToTest() {
+ $sets = [];
+
+ $sets[] = [
+ 'chado_integer_type_default',
+ ['feature_id','dbxref_id','organism_id','seqlen','type_id'],
+ ];
+
+ $sets[] = [
+ 'chado_boolean_type_default',
+ ['is_analysis', 'is_obsolete'],
+ ];
+
+ $sets[] = [
+ 'chado_string_type_default',
+ ['name'],
+ ];
+
+ $sets[] = [
+ 'chado_text_type_default',
+ ['uniquename','residues'],
+ ];
+
+ return $sets;
+ }
+
+ /**
+ * Tests adding a basic field type via the combined add field form.
+ * @dataProvider provideFieldsToTest
+ *
+ * This specifically refers to the form used in Drupal 10.2+ and thus
+ * will only be run on systems of the right Drupal version.
+ *
+ * NOTE: Debugging pages use the following
+ * - to get the full HTML: print $this->getSession()->getPage()->getContent();
+ * - to get the plain text without markup: print $this->getTextContent();
+ */
+ public function testCreateViaCombinedAddFieldForm($field_type_name, $valid_options) {
+
+ // ONLY do this test if we are in Drupal 10.2+ since we are assuming
+ // that the field storage + settings form are combined into a single page.
+ if (version_compare(\Drupal::VERSION, 10.2) < 0) {
+ $this->markTestSkipped('Test only applies to Drupal 10.2+');
+ }
+
+ // Pages to access.
+ $manage_fields_path = 'admin/structure/bio_data/manage/' . $this->type . '/fields';
+ $add_field_path = '/admin/structure/bio_data/manage/' . $this->type . '/fields/add-field';
+
+ // Details of the field to create.
+ $unique_suffix = uniqid();
+ $details = [
+ 'name' => 'basic_field_' . $unique_suffix,
+ 'label' => 'Test Basic Field ' . $unique_suffix,
+ ];
+
+ // Go to the manage fields admin page for the organism content type.
+ $html = $this->drupalGet($manage_fields_path);
+ $this->assertSession()->pageTextContains('Manage fields');
+ // Confirm there are no fields yet.
+ $this->assertSession()->pageTextContains('No fields are present yet.');
+
+ // Go to the page to add a new field to this content type.
+ $html = $this->drupalGet($add_field_path);
+ $this->assertSession()->pageTextContains('Add field');
+
+ // Step 1a: Field Name + Category
+ // Submit the form with the following input.
+ // We have no AJAX in these tests so we have to submit the form after selecting
+ // the category in order to see the list of field types in that category.
+
+ // Each key here indicates the form element to apply the value to.
+ // It can be either the id, name, label, or value of the form element.
+ $input = [
+ // The category of field we want to create.
+ // This is a collection of radio inputs in the form where all of them have the
+ // name=new_storage_type and the value indicates the storage type you want to select.
+ // To indicate a Chado Field we select the one where the category machine name=tripal_chado.
+ 'new_storage_type' => 'tripal_chado',
+ ];
+ $this->submitForm($input, 'Continue');
+
+ // Confirm that after submission, there
+ // -- is a form element with out field type.
+ // the id of the input element is the machine name of the field.
+ $form_element = $this->getSession()->getPage()->findById($field_type_name);
+ $this->assertNotNull($form_element,
+ "We were not able to find a form element with an id of $field_type_name after choosing the category.");
+
+ // Step 1b: Field Type
+ // Submit the form indicating the actual field type we want to create.
+ // This is another collection of radio inputs where the field machine name
+ // is the id of the input element.
+ $input = [
+ $field_type_name => $field_type_name,
+ ];
+ $this->submitForm($input, 'Continue');
+
+ // Step 1c: Actually indicate the name/label of our new field.
+ $input = [
+ // Machine name is a hidden input where the input name=field_name
+ 'field_name' => $details['name'],
+ // Field label is an input where the name=label
+ 'label' => $details['label'],
+ ];
+ $this->submitForm($input, 'Continue');
+
+ // Step 2: Fill in the Storage settings
+ // -- Confirm the field label is set from the previous step
+ $this->assertSession()->fieldValueEquals('label', $details['label']);
+ // -- Confirm the select list for base table is disabled and set properly.
+ $base_table_select = 'field_storage[subform][settings][storage_plugin_settings][base_table]';
+ $this->assertSession()->fieldDisabled($base_table_select);
+ $this->assertSession()->fieldValueEquals($base_table_select, 'feature');
+ // -- Confirm the select list base column exists + has the appropriate options.
+ $base_col_select = 'field_storage[subform][settings][storage_plugin_settings][base_column]';
+ $this->assertSession()->fieldEnabled($base_col_select);
+ foreach ($valid_options as $option) {
+ $this->assertSession()->optionExists($base_col_select, $option);
+ }
+ // Now fill out the remaining parts of this form.
+ // Each key here indicates the form element to apply the value to.
+ // It can be either the id, name, label, or value of the form element.
+ $input = [
+ $base_table_select => 'feature',
+ $base_col_select => $valid_options[0],
+ 'description' => 'This is the help text for the field.',
+ 'settings[field_term_fs][vocabulary_term]' => 'comment (schema:comment)',
+ ];
+ $this->submitForm($input, 'Save settings');
+
+ // Finally assert the field exists on the overview.
+ $this->assertFieldExistsOnOverview($details['label']);
+ }
+}

tripal_chado/tests/src/Functional/Plugin/Fields/CreateEditFieldForms/README.md

@@ -0,0 +1,9 @@
+
+# Purpose
+
+Tests in this directory are meant to test the process of
+- adding a Chado Field to an existing content type
+- editing the settings of an existing field on a specific content type
+
+More specifically, it tests the field_config_edit_form (D10.2+) and
+field_storage_config_edit_form (D10.1 and below).

tripal_chado/tripal_chado.module

@@ -53,7 +53,8 @@ function tripal_chado_config_schema_info_alter(&$definitions) {
  'label' => 'Entity Third Party Setting for Base Chado Table',
  'nullable' => true
  ];
- $definitions['tripal.content_type.*']['mapping']['third_party_settings']['sequence']['mapping']['chado_base_table'] = [
+
+ $definitions['tripal.content_type.*']['mapping']['third_party_settings']['mapping']['tripal']['mapping']['chado_base_table'] = [
  'type' => 'string',
  'label' => 'Entity Third Party Setting for Base Chado Table',
  'nullable' => true