Merge pull request tripal#1771 from tripal/tv4g2-issue1758-chado_cust…

…om_table_functionality

Tv4g2 issue1758 chado custom table functionality

tripal_chado/src/Services/ChadoCustomTableManager.php

@@ -2,17 +2,34 @@
 
 namespace Drupal\tripal_chado\Services;
 
-use Drupal\Core\Database\Database;
+use Drupal\Core\Database\Connection;
+use Drupal\tripal_chado\Database\ChadoConnection;
 use Drupal\tripal_chado\ChadoCustomTables\ChadoCustomTable;
 
 class ChadoCustomTableManager {
 
+  /**
+   * The Drupal database connection.
+   */
+  public Connection $connection;
+
+  /**
+   * The chado connection used to query chado.
+   */
+  public ChadoConnection $chado_connection;
+
 
   /**
    * Instantiates a new ChadoCustomTableManager object.
+   * 
+   * @param \Drupal\Core\Database\Connection
+   *  The database connection object.
+   * @param Drupal\tripal_chado\Database\ChadoConnection
+   *   The chado connection used to query chado.
    */
-  public function __construct() {
-
+  public function __construct(Connection $connection, ChadoConnection $chado_connection) {
+    $this->connection = $connection;
+    $this->chado_connection = $chado_connection;
   }
 
   /**
@@ -31,6 +48,8 @@ public function __construct() {
    * @return \Drupal\tripal_chado\ChadoCustomTables\ChadoCustomTable
    */
   public function create(string $table_name, string $chado_schema = NULL) {
+    // If the schema is not specified, get the default one.
+    $chado_schema = $this->chado_connection->schema()->getDefault();
     $custom_table = new ChadoCustomTable($table_name, $chado_schema);
     return $custom_table;
   }
@@ -45,9 +64,7 @@ public function create(string $table_name, string $chado_schema = NULL) {
    *   A ChadoCustomTable object or NULL if not found.
    */
   public function loadById(int $id) {
-    $public = \Drupal::database();
-
-    $query = $public->select('tripal_custom_tables','tct');
+    $query = $this->connection->select('tripal_custom_tables','tct');
     $query->fields('tct', ['table_name', 'chado']);
     $query->condition('tct.table_id', $id);
     $record = $query->execute()->fetchAssoc();
@@ -93,8 +110,11 @@ public function loadbyName(string $table_name, string $chado_schema = NULL) {
    */
   public function findByName(string $table_name, string $chado_schema = NULL) {
 
-    $public = \Drupal::database();
-    $query = $public->select('tripal_custom_tables','tct');
+    // Retrieve the default name of the Chado schema if it's not provided.
+    if ($chado_schema === NULL) {
+      $chado_schema = $this->chado_connection->schema()->getDefault();
+    }
+    $query = $this->connection->select('tripal_custom_tables','tct');
     $query->fields('tct', ['table_id']);
     $query->condition('tct.chado', $chado_schema);
     $query->condition('tct.table_name', $table_name);
@@ -115,8 +135,11 @@ public function findByName(string $table_name, string $chado_schema = NULL) {
   public function getTables(string $chado_schema = NULL) {
     $tables = [];
 
-    $public = \Drupal::database();
-    $query = $public->select('tripal_custom_tables','tct');
+    // Retrieve the default name of the Chado schema if it's not provided.
+    if ($chado_schema === NULL) {
+      $chado_schema = $this->chado_connection->schema()->getDefault();
+    }
+    $query = $this->connection->select('tripal_custom_tables','tct');
     $query->fields('tct', ['table_id', 'table_name']);
     $query->condition('tct.chado', $chado_schema);
     $query->orderBy('table_name');

tripal_chado/src/Services/ChadoMviewsManager.php

@@ -3,16 +3,24 @@
 namespace Drupal\tripal_chado\Services;
 
 use Drupal\Core\Database\Database;
+use Drupal\Core\Database\Connection;
+use Drupal\tripal_chado\Database\ChadoConnection;
 use Drupal\tripal_chado\ChadoCustomTables\ChadoMview;
 
 class ChadoMviewsManager extends ChadoCustomTableManager {
 
 
   /**
    * Instantiates a new ChadoCustomTableManager object.
+   * 
+   * @param \Drupal\Core\Database\Connection
+   *  The database connection object.
+   * @param Drupal\tripal_chado\Database\ChadoConnection
+   *   The chado connection used to query chado.
    */
-  public function __construct() {
-    parent::__construct();
+  public function __construct(Connection $connection, ChadoConnection $chado_connection) {
+    $this->connection = $connection;
+    $this->chado_connection = $chado_connection;
   }
 
   /**

tripal_chado/tests/src/Functional/Services/ChadoCustomTableManagerTest.php

@@ -0,0 +1,70 @@
+<?php
+
+namespace Drupal\Tests\tripal_chado\Functional;
+
+use Drupal\Core\Database\Database;
+use Drupal\Core\Test\FunctionalTestSetupTrait;
+use Drupal\tripal_chado\ChadoCustomTables\ChadoCustomTable;
+use Drupal\tripal_chado\Services\ChadoCustomTableManager;
+
+/**
+ * Tests the functions in the ChadoCustomTableManager services class.
+ * 
+ * @group Tripal
+ * @group Tripal Chado
+ */
+class ChadoCustomTableManagerTest extends ChadoTestBrowserBase {
+
+/**
+ *  Tests that we can create, list, and get custom table objects
+ * 
+ * @group chado
+ */
+  public function testCustomTableManager() {
+    // Create and then get the existing test chado schema name.
+    $this->createTestSchema(ChadoTestBrowserBase::INIT_CHADO_EMPTY);
+    $chado = \Drupal::service('tripal_chado.database');
+    $default_chado_schema = $chado->schema()->getDefault();
+
+    // Get an instance of the manager.
+    $ct_service = \Drupal::service('tripal_chado.custom_tables');
+
+    // Test that the manager was created successfully.
+    $this->assertInstanceOf(ChadoCustomTableManager::class, $ct_service, 'The Chado Custom Table Manager could not be created.');
+
+    // Test creating a table. The create() function returns a ChadoCustomTable object
+    $custom_table = $ct_service->create('test_custom_table', $default_chado_schema);
+
+    $this->assertInstanceOf(ChadoCustomTable::class, $custom_table, 'The test_custom_table could not be created');
+
+    // We created a table, let's load it by name.
+    $test_table_by_name = $ct_service->loadByName('test_custom_table', $default_chado_schema);
+
+    $this->assertInstanceOf(ChadoCustomTable::class, $test_table_by_name, 'The test_custom_table could not be created');
+
+    // Test loadById() with the id from the $test_table we just loaded. Make sure the returned tables are the same table object.
+    $test_table_by_id = $ct_service->loadById($test_table_by_name->getTableId());
+
+    $this->assertEquals($test_table_by_name, $test_table_by_id, 'Could not load the table by ID');
+
+    // Test the findByName() function. The returned int should match the ID found above by the table's getTableID() function.
+    $test_table_find = $ct_service->findByName('test_custom_table', $default_chado_schema);
+    $this->assertEquals($test_table_find, $test_table_by_name->getTableId(), 'Could not find the correct table');
+
+    // Test the getTables() function.
+    $expected_tables = [
+      '1' => 'test_custom_table',
+    ];
+    $tables = $ct_service->getTables($default_chado_schema);
+    $this->assertEquals($tables, $expected_tables, 'Could not get a list of tables from the ' . $default_chado_schema . ' schema.');
+    // Add another table
+    $custom_table = $ct_service->create('test_custom_table2', $default_chado_schema);
+    $expected_tables = [
+      '1' => 'test_custom_table',
+      '2' => 'test_custom_table2',
+    ];
+    $tables = $ct_service->getTables($default_chado_schema);
+    $this->assertEquals($tables, $expected_tables, 'Could not get a list of tables from the ' . $default_chado_schema . ' schema.');
+
+  }
+}

tripal_chado/tripal_chado.services.yml

@@ -8,8 +8,10 @@ services:
     arguments: ['@tripal_chado.database', '@tripal.logger']
   tripal_chado.custom_tables:
     class: Drupal\tripal_chado\Services\ChadoCustomTableManager
+    arguments: ['@database', '@tripal_chado.database']
   tripal_chado.materialized_views:
     class: Drupal\tripal_chado\Services\ChadoMviewsManager
+    arguments: ['@database', '@tripal_chado.database']
   tripal_chado.terms_init:
     class: Drupal\tripal_chado\Services\ChadoTermsInit
   tripal_chado.cloner: