Merge pull request #1552 from tripal/tv4g9-issue1546-chadoStorageTests

New infrastructure for Kernel Testing Chado Storage + Property Field Tests
tripal · Jun 27, 2023 · ed03c3a · ed03c3a
2 parents 4f42251 + 52c3232
commit ed03c3a
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Showing 5 changed files with 934 additions and 21 deletions.
diff --git a/tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php b/tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php
@@ -217,6 +217,8 @@ public function insertValues(&$values) : bool {
     $build = $this->buildChadoRecords($values, TRUE);
     $records = $build['records'];
 
+    // @debug print "Build Records: " . print_r($records, TRUE);
+
     $transaction_chado = $this->connection->startTransaction();
     try {
 
@@ -898,7 +900,7 @@ protected function buildChadoRecords($values, bool $is_store) {
             // entire record should be removed on an update and not inserted.
             $delete_if_empty = array_key_exists('delete_if_empty',$prop_storage_settings) ? $prop_storage_settings['delete_if_empty'] : FALSE;
             if ($delete_if_empty) {
-              $records[$chado_table][$delta]['delete_if_empty'][] = $key;
+              $records[$chado_table][$delta]['delete_if_empty'][] = $chado_column;
             }
           }
           if ($action == 'join') {

diff --git a/tripal_chado/tests/src/Functional/ChadoTestBrowserBase.php b/tripal_chado/tests/src/Functional/ChadoTestBrowserBase.php
@@ -79,26 +79,6 @@ protected function setUp() :void {
     }
   }
 
-  /**
-   * Returns the chado cvterm_id for the term with the given ID space + accession.
-   * This is completely independant of Tripal terms.
-   */
-  protected function getCvtermID($idspace, $accession) {
-
-    $connection = $this->getTestSchema();
-
-    $query = $connection->select('1:cvterm', 'cvt');
-    $query->fields('cvt', ['cvterm_id']);
-    $query->join('1:dbxref', 'dbx', 'cvt.dbxref_id = dbx.dbxref_id');
-    $query->join('1:db', 'db', 'db.db_id = dbx.db_id');
-    $query->condition('db.name', $idspace, '=');
-    $query->condition('dbx.accession', $accession, '=');
-    $result = $query->execute();
-
-    return $result->fetchField();
-
-  }
-
   /**
    * Creates an entity pre-loaded with the given genus and species.
    *

diff --git a/tripal_chado/tests/src/Functional/ChadoTestTrait.php b/tripal_chado/tests/src/Functional/ChadoTestTrait.php
@@ -65,6 +65,25 @@ trait ChadoTestTrait  {
    */
   protected static $db = NULL;
 
+  /**
+   * Returns the chado cvterm_id for the term with the given ID space + accession.
+   * This is completely independant of Tripal terms.
+   */
+  protected function getCvtermID($idspace, $accession) {
+
+    $connection = $this->getTestSchema();
+
+    $query = $connection->select('1:cvterm', 'cvt');
+    $query->fields('cvt', ['cvterm_id']);
+    $query->join('1:dbxref', 'dbx', 'cvt.dbxref_id = dbx.dbxref_id');
+    $query->join('1:db', 'db', 'db.db_id = dbx.db_id');
+    $query->condition('db.name', $idspace, '=');
+    $query->condition('dbx.accession', $accession, '=');
+    $result = $query->execute();
+
+    return $result->fetchField();
+
+  }
 
   /**
    * {@inheritdoc}