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I'd like to share WMS-WMTS links via GeoServer to the users; by using username and password system for accessing the layers with ArcGIS/QGIS and I'm having problem with the database connection to GeoServer right now.

So should I create user table with database and connect it directly to GeoServer with JDBC user group service ?

or am I able to make it in GeoServer's own website?

or is there any other solution for the encrypting?

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By default in GeoServer everyone (even no authenticated users) has access to the published data (read access) but only the administrator can change the data (write access).

You can configure through GeoServer web UI who can access your data: http://docs.geoserver.org/stable/en/user/security/webadmin/data.html

New users and groups can also be created through GeoServer web UI: http://docs.geoserver.org/stable/en/user/security/webadmin/ugr.html

You only need to configure the JDBC user group service if you don't want to use the default one.

Note that this allows you to define who will be able to read or write data, the data itself will not be encrypted.

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