def test_fetch_xray_pass(self): """fetch_xray()""" xray_fp = os.path.join(self.temp_dir, 'xray.yaml') fetch_xray(xray_fp) self.assertTrue(os.path.isfile(xray_fp)) expected = [ '101M', '102L', '102M', '103L', '103M', '104L', '104M', '105M', '106M', '107L', '107M', '108L', '108M', '109L', '109M', '10GS', '10MH' ] result = read_yaml(xray_fp) self.assertTrue(set(expected) < set(result)) return None
def fetch_and_write_files(dirs): """Fetch initial data files. Fetch data from remote servers and write to files if local files do not already exist. Fetches pdb_chain_uniprot.tsv, obsolete PDB files, and X-ray PDB files. Args: dirs (ProjectFolders): A named tuple of directory paths. Returns: None """ assert isinstance(dirs, ProjectFolders) assert os.path.isdir(dirs.project_home) assert dirs.uni_data assert dirs.tsv_data assert dirs.working # Run unit test for this manually to not overload servers. obs_fp = os.path.join(dirs.working, 'obs.yaml') if not os.path.exists(obs_fp): fetch_obsolete(obs_fp) # Run unit test for this manually to not overload servers. xray_fp = os.path.join(dirs.working, 'xray.yaml') if not os.path.exists(xray_fp): fetch_xray(xray_fp) # Run unit test for this manually to not overload servers. chain_fp = os.path.join(dirs.tsv_data, 'pdb_chain_uniprot.tsv') if not os.path.exists(chain_fp): fetch_pdb_chain_uniprot(chain_fp) return None