As expected this was an error in my application, specifically the META-INF/context.xml. I believe the url was incorrect in the Resource definition, and was thus being ignored. I also had a "id" element, which is not required.

My haste to consult StackOverflow was mainly because my payara wasn't showing any logging in my container, but this was a separate unrelated issue.

In summary, I was able to resolve with something akin to:

<Resource type="javax.sql.DataSource" 
    driverClassName="com.mysql.cj.jdbc.Driver"
    url="jdbc:mysql://172.0.0.1:3306/mydb"     
    username="user" 
    password="pass" 
    maxActive="20" 
    maxIdle="10" 
    maxWait="10000"/>