Реших проблема, както е описано тук:http://blog.netgloo.com/2015/07/09/spring-boot-communications-link-failure-with-mysql-and-hibernate/
, добавяйки тези конфигурации в application.properties
файл:
spring.datasource.tomcat.testWhileIdle = true
spring.datasource.tomcat.timeBetweenEvictionRunsMillis = 60000
spring.datasource.tomcat.validationQuery = SELECT 1