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Any jpql query containing current_timestamp in the select clause or where clause on Oracle uses the SYSDATE function instead of the SYSTIMESTAMP which means there will be no millis. This is due to to the code in OraclePlatform#initializePlatformOperators which overrides the TODAY operator set in DatabasePlatform#initializePlatformOperators. This can easily be fixed by providing the appropriate TODAY operator in Oracle9Platform#initializePlatformOperators to use the correct function to return the timestamp. As has been done for Oracle9Platform#getTimestampQuery.
The Eclipselink project has moved to Github: https://github.com/eclipse-ee4j/eclipselink