From the case summary:

The Obama administration moved to dismiss Jewel in 2009, claiming that litigation over the wiretapping program would require the government to disclose privileged “state secrets” and that it was immune from suit. The court instead ruled that the case should be dismissed on standing grounds. Fortunately, in December of 2011, the 9th U.S. Circuit Court of Appeals ruled that Plaintiffs’ allegations were sufficient to provide standing and Jewel could proceed in district court.

In July 2012, EFF moved to have the court declare that the FISA law applies instead of the state secrets privilege; in September, 2012 the government renewed its "state secrets" claims and the matter was heard by the federal district court in San Francisco on Dec. 14, 2012.

I am surprised that they survived a motion regarding the plaintiff's standing.