Fixes for database and setup commands (CFM-535)

app/src/Application.php

@@ -90,7 +90,7 @@ public function bootstrap(): void
                 $this->addPlugin($p->plugin);
             }
         }
-        catch(\Cake\Database\Exception\DatabaseException $e) {
+        catch(\Cake\Database\Exception\QueryException | \Cake\Database\Exception\DatabaseException $e) {
             // Most likely we are performing the initial database setup and
             // the plugins table is missing.
         }

app/src/Command/SetupCommand.php

@@ -148,7 +148,7 @@ public function execute(Arguments $args, ConsoleIo $io)
       'co_id'   => $co_id,
       'status'  => SuspendableStatusEnum::Active
     ],
-    ['validate' => false]);
+    ['validate' => false, 'skipNormalization' => true]);
 
     $person->names = [$coTable->People->Names->newEntity([
       'type_id'       => $coTable->Types->getTypeId(coId:       $co_id, 
@@ -158,7 +158,7 @@ public function execute(Arguments $args, ConsoleIo $io)
       'family'        => $sn,
       'primary_name'  => true
     ],
-    ['validate' => false])];
+    ['validate' => false, 'skipNormalization' => true])];
 
     $person->identifiers = [$coTable->People->Identifiers->newEntity([
       'type_id'       => $coTable->Types->getTypeId(coId:       $co_id, 
@@ -168,7 +168,7 @@ public function execute(Arguments $args, ConsoleIo $io)
       'login'         => true,
       'status'        => SuspendableStatusEnum::Active
     ],
-    ['validate' => false])];
+    ['validate' => false, 'skipNormalization' => true])];
 
     $person->person_roles = [$coTable->People->PersonRoles->newEntity([
       'affiliation_type_id'   => $coTable->Types->getTypeId(coId:       $co_id, 
@@ -177,18 +177,18 @@ public function execute(Arguments $args, ConsoleIo $io)
       'title'                 => __d('command', 'se.person_role.title'),
       'status'                => SuspendableStatusEnum::Active
     ],
-    ['validate' => false])];
+    ['validate' => false, 'skipNormalization' => true])];
 
     $g = $coTable->Groups->find('adminGroup', co_id: $co_id)->firstOrFail();
 
     $person->group_members = [
       $coTable->People->GroupMembers->newEntity(
         ['group_id' => $g->id],
-        ['validate' => false]
+        ['validate' => false, 'skipNormalization' => true]
       ),
       $coTable->People->GroupMembers->newEntity(
         ['group_id' => $g->owners_group_id],
-        ['validate' => false]
+        ['validate' => false, 'skipNormalization' => true]
       )
     ];
 

app/src/Model/Behavior/NormalizationBehavior.php

@@ -64,9 +64,11 @@ public function beforeMarshal(Event $event, ArrayObject $data, ArrayObject $opti
 
     // We need the CO for the record in order to find the appropriate configuration(s) to use,
     // but for that we need $data in entity form.
-
     // This will recurse, so make sure to break the loop
-    $entity = $Table->newEntity((array)$data, options: ['skipNormalization' => true]);
+    $entity = $Table->newEntity(
+      (array)$data,
+      options: [...$options, 'skipNormalization' => true]
+    );
 
     $coId = $Table->calculateCoForRecord($entity);