You mention that she has been throwing up bile, has dark urine and from what you additionally mention she is having problems fully emptying her bladder while urinating. With all of these things going on she absolutely needs to be seen by your vet~today.
I'm not a vet but I could take a guess and she possibly might have a UTI. But only your set will be able to diagnose and treat her properly. Please keep us posted on what the vat has to say. Good Luck!
