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
