Urinating in crate/Barking in crate

Question
I have a 12 week old Blue Doberman which was rescue from the shelter. I have been trying to crate train him for the past 4 weeks, but it's hasn't been to successful. He will urinate in the crate, but he won't poop. I took him to the vet and discovered he had a urinary tract infection. I gave him the medicine for 2 weeks, but he still urinate in the crate. Could you please help me with this problem? When I put him in the crate he barking all the time. What am I doing wrong? I want him to be a house dog, but the constant urinating is a big problem.

Answer
Well what a lot of people use when a crate fails is to confine the dog in one room and put down puppy pads or papers,and how that works is just before the puppy is going to urinate,place the puppy on the paper/pad,and after just a couple of times the puppy will go on the paper/pad and slowly move it closer to the door and that will move them outside