Optical networks are moving from opaque and translucnet architectures towards all-optical (transparent) architecutres. In translucent architectures a small amount of regeneration (e.g. optical-electronic-optical conversion) is available in the network. The incorporation of the physical impairments in the routing and wavelenghth assignment (RWA) problem in transparent optical networks has recently received some attention from the research communities. this work compiles a comprehensive survey of the proposed algorithms that address this issue. the physical layer impairments and related classification in optical networks are initially presented followed by physical layer impairments (PLI) constrained and aware RWA algorithms. Algorithmic approach, current PLI-RWA proposals, impact of wavelenght conversation on these algorithms, protection and resilience considerations, and proposed extensions to control planes are covered in this work. Further research topics are presented in this study.