A Cook County judge Thursday left intact the majority of a lawsuit seeking to overturn the city’s controversial food truck ordinance.

In letting the lawsuit proceed, Judge Peter A. Flynn said he is “uncomfortable” with a provision of the ordinance that requires food trucks to install GPS systems so the city can track their whereabouts.

“It is not clear . . . how the city proposes to protect against the misuse of the data (collected),” Flynn said, in making his ruling.