Fix remaining bugs in make_json_model refactor.
Fix remaining bugs in make_json_model refactor.

bgyori/indra,johnbachman/indra,sorgerlab/belpy,bgyori/indra,sorgerlab/indra,johnbachman/indra,sorgerlab/belpy,sorgerlab/indra,sorgerlab/belpy,johnbachman/indra,sorgerlab/indra,bgyori/indra