I'm currently new to web developing and right now I started with a Spring Boot application which I converted to standard App Engine project. I'm wondering if it is possible to not convert my Spring Boot application to my App Engine project and still use Datastore as database?
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Yes, it's possible to use the Cloud Datastore from an app in the GAE flexible environment, from outside GAE or even from outside the Google Cloud. From Cloud Datastore (emphasis mine):
But you can't use the GAE Standard Environment Client Libraries, you have to use either the Cloud Datastore Client Libraries or the Cloud Datastore API v1.
Potentially of interest: the Deploying to the App Engine Flexible Environment guide happens to use a spring boot app as example.