Merge pull request #1535 from reynoldtan/tv4g2-issue1534-chadoCvtermA…

…utocompleteUpdate Tv4g2 issue1534 chado cvterm autocomplete update
tripal · Jun 2, 2023 · 73c091e · 73c091e
2 parents a07fea6 + b9a93dd
commit 73c091e
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diff --git a/tripal_chado/src/Controller/ChadoCVTermAutocompleteController.php b/tripal_chado/src/Controller/ChadoCVTermAutocompleteController.php
@@ -105,4 +105,38 @@ public static function getCVtermId(string $term): int {
 
     return $id;
   }
+
+  /**
+   * Given a cvterm id number, return the matching cvterm record using
+   * the format cvterm name (db.name:dbxref.accession).
+   * 
+   * @param integer $id
+   *   Cvterm id number to match.
+   * 
+   * @return string
+   *   Cvterm record in cvterm name (db.name:dbxref.accession) format.
+   */
+  public static function formatCVterm(int $id) {
+    $term = null;
+
+    if ($id > 0) {
+      $sql = "
+        SELECT CONCAT(ct.name, ' (', db.name, ':', 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.cvterm_id = :cvterm_id
+        LIMIT 1 
+      ";
+
+      $connection = \Drupal::service('tripal_chado.database');
+      $result = $connection->query($sql, [':cvterm_id' => $id]);
+
+      if($result) {
+        $term = $result->fetchField();
+      }
+    }
+
+    return $term;
+  }
 }
diff --git a/tripal_chado/tests/src/Functional/Controller/ChadoTableCvtermAutocompleteTest.php b/tripal_chado/tests/src/Functional/Controller/ChadoTableCvtermAutocompleteTest.php
@@ -118,5 +118,18 @@ public function testAutocompleteCvterm() {
       $id = $autocomplete->getCVtermId($i);
       $this->assertEquals($id, 0);
     }
+
+
+    // Test format CVterm method.
+    foreach(json_decode($suggest) as $item) {
+      // ChadoCVTermAutocompleteController::getCVtermId()
+      $id = $autocomplete->getCVtermId($item->value);
+      // Reverse value - get formatted term.
+      $term = $autocomplete->formatCVterm($id);
+
+      $this->assertNotNull($term);
+      $this->assertIsString($term);
+      $this->assertEquals($term, $item->value);
+    }
   }
 }