What isolation level should you be aiming for when automating your scenarios? Should they be completely isolated, as with proper unit tests (ie using mocks etc), or are they more akin to integration tests?
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Scenarios are typically on the level of integration tests.
Ideally scenarios are used in communication with the customer, or at least use the terms and language of the customer. A passing scenario provides concrete evidence that the software does what the customer wants. The customer does not care about individual components, but about the system as a whole.
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Lunivore
As a note, an integration test might be smaller - for instance, you could check that a message constructed by a webservice can be received and parsed by the client, without testing the whole system.