For all I know (I'm not a lawyer) that's exactly what happened. The article that said the warrants were obtained from a secret court may have meant that the proceedings were classified as you mentioned. The use of the words "secret court" may just be the reporters attempt to cast this in the worst possible light. The President has said the NSA obtained legal authority to do what it did, the decisions were reviewed by the Justice Dept, White House legal council and NSA legal council and in addition appropriate members of congress were kept in the loop on a frequent basis. I'm giving the President the benefit of the doubt. Knowing how the Democratic smear machine works I won't believe a thing they say unless they can get a ruling from the Supreme Court supporting their allegations.