def test_force_fetch_obsolete_pass(self):
"""fetch_obsolete()"""
obs_fp = os.path.join(self.temp_dir, 'obs.yaml')
with open(obs_fp, 'w', encoding='utf-8') as obs_fh:
obs_fh.write("\n")
fetch_obsolete(obs_fp, force_download=True)
expected = {'1E6T', '1E7T', '1E7X'}
result = read_yaml(obs_fp)
self.assertLess(expected, set(result))
def test_fetch_obsolete_from_servers(self):
expected = {
"2TNA", "2TNC", "2UCE", "2UV9", "2UVA", "2UVB", "2UVC",
"2UWG", "2UWY", "2UWZ", "2V0Q", "2V2Y", "2V44", "2V46"
}
obs_fp = os.path.join(self.temp_dir, 'obs.yaml')
fetch_obsolete(obs_fp)
self.assertTrue(expected < set(read_yaml(obs_fp)))
return None
def test_fetch_pdb_chain_pass(self):
"""test fetch_pdb_chain_uniprot() when file exists."""
chain_fp = os.path.join(self.temp_dir, 'pdb_chain_uniprot.tsv')
with open(chain_fp, 'w', encoding='utf-8') as chain_fh:
chain_fh.writelines("\n")
with captured_stdout() as stdout:
fetch_obsolete(chain_fp)
result = stdout.getvalue().strip()
self.assertTrue(self.success_msg.search(result))
return None
def test_fetch_xray_pass(self):
"""Test fetch_xray() when file exists."""
xray_fp = os.path.join(self.temp_dir, 'xray.part.yaml')
with open(xray_fp, 'w', encoding='utf-8') as xray_fh:
xray_fh.writelines("\n")
with captured_stdout() as stdout:
fetch_obsolete(xray_fp)
result = stdout.getvalue().strip()
self.assertTrue(self.success_msg.search(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
