I was using IntelliJ Idea 2018.3.3 IDE and not sure if Gradle build will work in your set-up.
For me it worked only from Gradle toolbar -> tasks -> build -> build
Feel free to execute script run_jar.sh that runs jar with necessary parameters.
My solution sets the alert flags for events that last longer than 4 ms independently of their order.
Running HSQLDB Server in separate thread.
Using Google GSON library to parse JSON, that theoretically doesn't impose any limits to the file size. Unfortunately I didn't have time to look deeper and properly stress-test the program.
Using Hibernite and JPA to query and persist to database.
Using one Entity - ServerLogEntry that is shared between Google GSON and JPA classes.
Have configuration classes to change Anomaly Detection Rules and connection parameters