For join datatypes, the parent allows re-indexing/adding/deleting specific children. However, using has_child or has_parent queries can have a significant impact on performance. If you need better performance, always use nested datatypes. Nonetheless, as long as you have to update, you need to re-index all children to their parent. The nested datatype approach is also easier to manage than the join datatype approach. You must be very careful while using the join datatype method because you can index children without a parent. Also, if you want to remove a parent, it is not an automatic cascading task to delete all of its children. You need to clean it up by yourself. On the other hand, if you want to update parent or child document, the join datatypes approach will be more convenient because you can update the values in the parent field or the child field...
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