Update

[zhengj2007]

Handle 'na' values in the conversion file and detect IRI and label of term/parent positions in the file based on column header, no need to set in the setting file.

[johnwjudkins]

I've tested the jar file, and it works, but I see that you replaced
private String settingFilename = "./test/setting.txt";
with
private String settingFilename = "/Users/jiezheng/Documents/VEuPathDB-git/ApiCommonData/Load/ontology/script/test-local/setting_test.txt";
in src/ontoTool/OntologyClassGeneratorOptions.java.
Do you want a relative path here instead of the full path?

[zhengj2007]

You can ignore it. It is the value I set for testing. No change for people to run the script. Both full path and relative one are working.