EDIT:Med alle de nye data forstår jeg tydeligt, hvad du forsøger at opnå.
Så jeg redigerede min gamle funktion, dette er en ny, der burde fungere lige i din kode. Giv mig besked, så jeg kan justere, hvis det er nødvendigt.
public function setCategories($user_id)
{
$api = new ApiCategory($user_id);
$cats = $api->getCategories(); // retrieves structure above
$newCats = null;
self::recursiveCatTree($newCats, $cats);
$this->categories = $newCats;
$this->save(); // save the entire array of embedded documents
if($this->getErrors())
var_dump($this->getErrors);
}
public static function recursiveCatTree(&$result, $parent)
{
$children = $parent['children'];
//we unset the children so we dont have manually set every other variable
unset( $parent['children']);
$result = new Category();
$result->attributes = $parent;
//then loop the children, if no children it wont loop
// so it will just be an empty array
foreach($children as $child)
{
$baby = null;
self::recursiveCatTree($baby, $child);
$result->children[] = $baby;
}
}