Hi @MICHAEL ,
For the MSSQL database, as you said, you can use EntityFramework (EF) or EntityFramework Core (EF core) to access the database, and then use a dbcontext to access the data table and get the data.
For the Sybase database, I'm not sure whether you can use EF or EF core to access it or not, because from the EF core Database Providers, it doesn't contain the provider for the Sybase database. You might need to create custom provider and use it. Here is an article about How to connect to Sybase database from .net core, it will use the ADO.NET method to query the database.
So, you could use two dbcontext (if you can access the Sybase via the EF/EF core) or use one dbcontext for MS SQL Server database and use ADO.NET method for the Sybase database.
Then create user authentication and authorization in MSSQL
Agree with AgaveJoe, you can create JWT Authentication in Web API.
After fetching data from two databases respectively (using two dbcontext or one dbcontext and one Ado.net query result), you can use LINQ Query Operations to query the data and check whether the login user is a valid user or not, Then, generate a JWT token to do the authentication and authorization.
You can refer the following articles:
JWT Authentication In ASP.NET Core
ASP.NET Core Web API 5.0 Authentication Using JWT(JSON BASE TOKEN)
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Best regards,
Dillion