I have a multi tenant application which I am trying to deploy on Azure using a web app package.
When a user registers for a new account at that moment a database is created for them and this works flawlessly on my development machine with SQL Server 2014.
Do I need to configure the database server on Azure to allow this, if so how?
Not creating the database may be caused by a timeout. See this post: Entity Framework Database Initialization: Timeout when initializing new Azure SqlDatabase
If you need a new database to be created when someone signs up, you can better create the database before firing up Entity Framework.
This can be done using either T-SQL (1) when connected to the master database of your server or using the Azure Sql Managment Libraries (2). I would recommend option two since it will allow you to depend on a nice abstraction rather than interacting with the database directly.
1: https://msdn.microsoft.com/en-us/library/dn268335.aspx
2: https://www.nuget.org/packages/Microsoft.Azure.Management.Sql
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