You need to configure the programming mode to "Power Cycle". When using PSoC programmer it is an option on main window. When using Creator you need to set the miniprog3 properties accordingly.
//I am wondering if it is possible to programm the chip using only SWDIO and SWDCLK?// When you are using power cycle mode make sure that you are not externally powering the device. Power Cycle programming mode toggles the power to the device to acquire device. Thus, this should be used when the device is not powered externally. MiniProg should be able to apply supply to the device in this case, so connect VDD pin of the device to VTARG of the miniprog.
You can use read this document for more details :http://www.cypress.com/file/126826/download