The following message is returned when connecting from ArcGIS Server on Ubuntu to a SQL Server database:
arcgisscripting.ExecuteError: ERROR 000110: <path to database connection file>/<filename>.sde does not exist
This message is returned when there is a problem with the SQL Server ODBC communication with the database. Specifically, when ArcGIS Server is installed on Ubuntu and cannot connect to SQL Server databases, the problem is usually that the database uses an unsupported Secure Hash Algorithm for encryption with self-signed certificates.
By default, SQL Server 2016 and earlier releases use Secure Hash Algorithm-1 (SHA-1) for encryption. SHA-1 has been deprecated. ArcGIS Server cannot connect to databases that still use this algorithm for encryption with self-signed certificates.
Update the SHA version used by the database.