They will not run a drug use test, no. They will simply test your urine for the presence of blood cells and bacteria (indicating infection).
MDMA can cause kidney problems, though, especially if you don't drink enough water while on it. So be careful in the future. There is a fine balance - you need to be hydrated, but NOT TOO MUCH, as MDMA impairs kidney function sometimes and people can get "water poisoning".
MDMA can be safe, but you need to know what you are doing. Even if they do test for drugs, under confidentiality laws, the dr. can't tell anyone except you, anyway.
They will, of course, ask you sexual questions, so don't be surprised or offended. Health professionals do not judge you, they just need accurate information to help you get better.