In short - today there is no easy way to do this.
Chrome has a discussion here: https://code.google.com/p/chromium/issues/detail?id=402223
Last comment of October 2015:
To date, the safest minimum solution for sites is to abandon the mechanism (which we strongly recommend that you do in any case!), So users can turn off notifications from one platform
Another possible heuristic decision is to take a certain measure for which interface (website or native) the user most often uses (or most have recently used) and only send it to it. In combination with the grouping of these devices with a rough screen size should give a pretty good approximation.
The problem is that if the user has two devices with the same size and uses the native one on one, and the web on the other, then notifications will only be delivered to one, which is an edge case.
We also discussed creating an API so that sites can determine if their respective native application is installed in order to avoid this, but you need to start discussing this with other browser providers to find out if they will support it.
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