def test_fetch_pdb_chain_from_server_pass(self):
expected = re.compile(r'(\w+\t\w{1,2}\t\w+\t(\d+[\t\n]){6,})')
chain_fp = os.path.join(
self.temp_dir,
'pdb_chain_uniprot.tsv')
fetch_pdb_chain_uniprot(chain_fp)
with open(chain_fp, 'r', encoding='utf-8') as chain_fh:
for line in chain_fh.readlines()[3:10]:
self.assertTrue(expected.search(line))
return None
def test_fetch_pdb_chain_original_pass(self):
result_fp = join(
self.temp_dir,
'pdb_chain_uniprot.tsv'
)
expected_fp = join(
self.test_data_dp,
'data',
'pdb_chain_uniprot.tsv.expected'
)
# print(expected_fp)
fetch_pdb_chain_uniprot(result_fp)
self.assertTrue(cmp(expected_fp, result_fp, shallow=False))
return None
def test_fetch_pdb_chain_existing_file_pass(self):
"""fetch_pdb_chain_uniprot with existing file"""
success_msg = re.compile(
r'^Found local copy of.*',
re.IGNORECASE
)
chain_fp = os.path.join(
self.test_data_dp,
'data',
'initial_filtering_data',
'tsv_data',
'pdb_chain_uniprot.tsv')
with captured_stdout() as stdout:
fetch_pdb_chain_uniprot(chain_fp)
result = stdout.getvalue().strip()
print(result)
self.assertTrue(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
