workaround for the fact that RefreshDatabase does not handle debugging gt db; pseduo-migrate it...

Author: bpow

tests/Feature/End2End/Groups/PublishApplicationEventsTest.php

@@ -152,7 +152,7 @@ private function addPerson()
         ]);
     }
 
-    private function addGene($genes = null)
+    private function addGene()
     {
         $genes = $this->seedGenes([['hgnc_id' => 678, 'gene_symbol'=>'BCD'], ['hgnc_id' => 12345, 'gene_symbol' => 'ABC1']]);
         $action = app()->make(GenesAdd::class);

tests/Traits/SeedsHgncGenesAndDiseases.php

@@ -26,7 +26,23 @@ private function seedDiseases($diseases = null)
 
     private function getDb()
     {
-        return DB::connection(config('database.gt_db_connection'));
+        $conn = DB::connection(config('database.gt_db_connection'));
+        // This is an ugly hack for the fact that RefreshDatabase doesn't work with multiple connections
+        // The real fix would be to access genetracker only through an API (and to mock it appropriately)
+        if (!$conn->getSchemaBuilder()->hasTable('genes')) {
+            $conn->getSchemaBuilder()->create('genes', function($table){
+                $table->biginteger('hgnc_id');
+                $table->string('gene_symbol');
+            });
+        }
+        if (!conn->getSchemaBuilder()->hasTable('diseases')) {
+            $conn->getSchemaBuilder()->create('diseases', function($table){
+                $table->bigIncrements('id');
+                $table->string('mondo_id');
+                $table->string('name');
+            });
+        }
+        return $conn;
     }