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If we are running two different node instance one of each purpose( webservice engine/data engine and webservice consumer) will it be good or keeping both the purpose in same application will be better ?

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Yes it is.

One project is your API, the second project is the access to your API by web.

Maybe in the future you might need a mobile app to connect with the API or maybe the webapp technology becomes obsolete and you might need to replace it for another modern technology, so that you don't have to change your API.

Sergio Marcelino
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