The working steps to connect with JDBC connector with ssl.
Select Connection Type JDBC, in the url parameter, add:
Jdbc:mysql://127.0.0.1:3306/sample?verifyServerCertificate=false&useSSL=true&requireSSL=true
Replace 127.0.0.1:3306 with the url to your actual server, and replace sample with the name of the database you want to use within this server.
Setting verifyServerCertificate to false allows you to use self signed certificates. The other parameters are self explanatory and should match the settings on your server.
If you created your Base document with version 6.x and newer, your linked subforms might stop working. Solution from this post :
Edit > Database > Advanced Settings > Replace named parameters with ‘?’ (Checked)
For those interested in this post, and (like me) not understanding very well how certificates work, this might help.
After successfully connecting to the database, I was worried about not specifying the path to the clients certificate in the process. This page on the mysql website helped me understand it a little better.
To sum up what I understand ( I have no expertise, and might be wrong) there are two ways of connecting with ssl. Which way you are using depend on how you created the user (logins you are using) in the mysql server. If you did not specify upon user creation that the user has to present its own certificates, the connection will still be encrypted by the server.
If you did specify that the user has to present the certificates, then you are using what the linked page above refers to as 2-Way Authentication, and you do need to point to the ssl certificates client-side. I have no idea how to set that up with Base and would be interested if someone knew.
Thanks Ratslinger for your help.