I am reading the configuration reference for the JanusGraph https://docs.janusgraph.org/0.2.0/config-ref.html and I wonder - in which file should I write those values? Under conf directory of the JanusGraph there is no single common file in which I can write those options. I am so confused and documentation does not specify it!
These configuration options should be put into a .properties configuration file. The JanusGraph distribution zip archive already contains example configuration files for different backends that can be used as a basis, for example for Cassandra with Elasticsearch: conf/janusgraph-cql-es.properties.
How these configuration files are provided to JanusGraph depends on whether you want to use JanusGraph embedded or via JanusGraph Server (which is the recommended approach). If you want to use JanusGraph Server, then you need a section that specifies this configuration file for JanusGraph in the configuration file of the server which is conf/gremlin-server/gremlin-server.yaml by default:
graphs: {
graph: conf/janusgraph-cql-es.properties
}
The chapter Using Configuration of the JanusGraph docs contains more information about how the configuration can be applied.