Merge pull request #1486 from reynoldtan/tv4g2-issue1482-chadoCvtermA…

…utocomplete

Chado CV Term Autocomplete Functionality

tripal_chado/src/Controller/ChadoCVTermAutocompleteController.php

@@ -0,0 +1,108 @@
+<?php
+
+namespace Drupal\tripal_chado\Controller;
+
+use Drupal\Core\Controller\ControllerBase;
+use Symfony\Component\HttpFoundation\Request;
+use Symfony\Component\HttpFoundation\JsonResponse;
+
+/**
+ * Controller routines for the chado CV Term autocomplete.
+ */
+class ChadoCVTermAutocompleteController extends ControllerBase {
+  /**
+   * Contoller method, autocomplete cvterm name.
+   * 
+   * @param Request request
+   * @param int $cv
+   *   @TODO: Limit the match of term to a CV.
+   * @param int $count
+   *   Desired number of matching names to suggest.
+   *   Default to 5 items.
+   * 
+   * @return Json Object
+   *   Matching cvterm rows where each row is formatted as string:
+   *   cvterm.name (db.name:dbxref.accession) and is the value for
+   *   the object keys label and value.
+   */
+  public function handleAutocomplete(Request $request, int $count = 5) {
+    // Array to hold matching cvterm names.
+    $response = null;
+
+    if ($request->query->get('q')) {
+      // Get typed in string input from the URL.
+      $string = trim($request->query->get('q'));
+
+      if (strlen($string) > 1 && $count > 0) {
+        // Proceed to autocomplete when string is at least 2 characters
+        // long and result count is set to a value greater than 0.
+
+        // Transform string as a search keyword pattern.
+        $keyword = '%' . strtolower($string) . '%';
+
+        // Query cvterm (joins: dbxref - accession and db - dn name) for names matching 
+        // the keyword pattern and return each row in the format specified. 
+        // Tables indicate schema sequence number #1 to use default schema.
+        $sql = sprintf("
+          SELECT ct.name AS term, db.name AS dbname, dx.accession
+          FROM {1:cvterm} AS ct 
+            LEFT JOIN {1:dbxref} AS dx USING(dbxref_id) 
+            LEFT JOIN {1:db} USING(db_id)
+          WHERE ct.name LIKE :keyword ORDER BY ct.name ASC LIMIT %d
+        ", $count);
+
+        // Prepare Chado database connection and execute sql query by providing value 
+        // for :keyword placeholder text.
+        $connection = \Drupal::service('tripal_chado.database');
+        $results = $connection->query($sql, [':keyword' => $keyword]);  
+
+        // Compose response result.
+        if ($results) {
+          foreach ($results as $record) {
+            $term = $record->term . ' (' . $record->dbname . ':' . $record->accession . ')';
+            $response[] = [
+              'value' => $term, // Value returned and value displayed by textfield.
+              'label' => $term  // Value shown in the list of options.
+            ];
+          }
+        }
+      }
+    }
+
+    return new JsonResponse($response);
+  }
+
+  /**
+   * Fetch the cvterm.cvterm_id given a cvterm name (db.name:dbxref.accession)
+   * value returned by the handler method above.
+   * 
+   * @param string $term
+   *   String value returned by authocomplete handler method. 
+   * 
+   * @return integer
+   *   Id number corresponding to chado.cvterm_id field of the matching term
+   *   or 0 if no match was found.
+   */
+  public static function getCVtermId(string $term): int {
+    $id = 0;
+
+    if (strlen($term) > 0) {
+      $sql = "
+        SELECT ct.cvterm_id FROM {1:cvterm} AS ct 
+          LEFT JOIN {1:dbxref} AS dx USING(dbxref_id) 
+          LEFT JOIN {1:db} USING(db_id)
+        WHERE CONCAT(ct.name, ' (', db.name, ':', dx.accession, ')') = :term
+        LIMIT 1 
+      ";
+
+      $connection = \Drupal::service('tripal_chado.database');
+      $result = $connection->query($sql, [':term' => $term]);
+
+      if($result) {
+        $id = $result->fetchField();
+      }
+    }
+
+    return $id;
+  }
+}

tripal_chado/tests/src/Functional/Controller/ChadoTableCvtermAutocompleteTest.php

@@ -0,0 +1,122 @@
+<?php
+
+namespace Drupal\Tests\tripal_chado\Functional;
+
+use Drupal\Tests\tripal_chado\Functional\ChadoTestBrowserBase;
+use Drupal\tripal_chado\Controller\ChadoCVTermAutocompleteController;
+use Symfony\Component\HttpFoundation\Request;
+
+/**
+ * Test autocomplete cvterm name.
+ */
+class ChadoTableCvtermAutocompleteTest extends ChadoTestBrowserBase {
+  /**
+   * Registered user with access content privileges.
+   * 
+   * @var \Drupal\user\Entity\User
+   */
+  private $registered_user;
+
+
+  /**
+   * Test autocomplete cvterm name.
+   */
+  public function testAutocompleteCvterm() {
+    // Setup registered user.
+    $this->registered_user = $this->drupalCreateUser(
+      ['access content'],
+    );
+
+    $this->drupalLogin($this->registered_user);
+
+    // Ensure we see all logging in tests.
+    \Drupal::state()->set('is_a_test_environment', TRUE);
+
+    // Create a new test schema for us to use.
+    $connection = $this->createTestSchema(ChadoTestBrowserBase::PREPARE_TEST_CHADO);
+
+    // Test Handler:
+    $autocomplete = new ChadoCVTermAutocompleteController();
+    // Prepare a Request:$request entry. Search for null term
+    // and suggest at least 5 items.
+    $request = Request::create(
+      'chado/cvterm/autocomplete/5',
+      'GET',
+      ['q' => 'null']
+    );
+
+    $suggest = $autocomplete->handleAutocomplete($request)
+      ->getContent();
+
+    // Find if null cvterm was suggested.
+    $null_found = 0;
+    foreach(json_decode($suggest) as $item) {
+      if (str_contains($item->value, 'null')) {
+        $null_found++;
+      }
+    }
+
+    $this->assertTrue($null_found > 0);
+
+
+    // Test Get Id.
+    // Each item in the result for term null should have
+    // an integer value which is the cvterm id number.
+    foreach(json_decode($suggest) as $item) {
+      // ChadoCVTermAutocompleteController::getCVtermId()
+      $id = $autocomplete->getCVtermId($item->value);
+
+      $this->assertNotNull($id);
+      $this->assertIsInt($id);
+    }
+
+
+    // Test limit.
+    $request = Request::create(
+      'chado/cvterm/autocomplete/5',
+      'GET',
+      ['q' => 'ul']
+    );
+    // This will return > 6 terms ie. n[ul]l, vocab[ul]ary, pop[ul]ation, form[ul]a etc.
+    // but should only suggest exactly 6 items.
+
+    $suggest = $autocomplete->handleAutocomplete($request, 6)
+      ->getContent();
+
+    $this->assertEquals(count(json_decode($suggest)), 6);
+
+
+    // Test exact term and 1 suggestion (exact match).
+    $query = $connection->select('1:cvterm', 'c');
+    $query->condition('c.name', 'null', '=');
+    $query->fields('c', ['cvterm_id']);
+    $null_cvterm_id = $query->execute()->fetchField();
+
+    $request = Request::create(
+      'chado/cvterm/autocomplete/5',
+      'GET',
+      ['q' => 'null']
+    );  
+
+    $suggest = $autocomplete->handleAutocomplete($request, 1)
+      ->getContent();
+
+    foreach(json_decode($suggest) as $item) {
+      // ChadoCVTermAutocompleteController::getCVtermId()
+      $id = $autocomplete->getCVtermId($item->value);
+
+      $this->assertNotNull($id);
+      $this->assertIsInt($id); 
+      $this->assertEquals($id, $null_cvterm_id);
+    }
+
+
+    // Test invalid values as id passed to GetId.
+    // Not found
+    $not_ids = [0, 'lorem.ipsum', 'null', '@$#%', 'null (abc:xyz)', ' ', '.'];
+    foreach($not_ids as $i) {
+      $id = $autocomplete->getCVtermId($i);
+      $this->assertEquals($id, 0);
+    }
+  }
+}

tripal_chado/tripal_chado.routing.yml

@@ -135,4 +135,14 @@ entity.chado_term_mapping.delete_form:
     _entity_form: 'chado_term_mapping.delete'
     _title: 'Delete Mapping'
   requirements:
-    _permission: 'administer tripal'
+    _permission: 'administer tripal'
+
+
+tripal_chado.cvterm_autocomplete:
+  path: 'chado/cvterm/autocomplete/{count}'
+  defaults:
+    _controller: '\Drupal\tripal_chado\Controller\ChadoCVTermAutocompleteController::handleAutocomplete'
+    _title: 'Chado Vocabulary Term Autocomplete'
+    _format: json
+  requirements:
+    _permission: 'access content'