def test_only_one_include():
# This is formatted strangely because pep8 says so.
with \
TemporaryDirectory() as data,\
TemporaryDirectory() as out:
with pytest.raises(AssertionError, match='Only one'):
sct_run_batch.main([
'-include', 'arg', '-include-list', 'arg2', '-path-data', data,
'-path-out', out, '-script', out
])
def test_only_one_include(tmp_path, dummy_script):
"""
Test that an error is thrown for trying to pass both '-include' and '-include-list' at the same time.
"""
data = tmp_path / 'data'
data.mkdir()
out = tmp_path / 'out'
with pytest.raises(AssertionError, match='Only one'):
sct_run_batch.main([
'-include', 'arg', '-include-list', 'arg2', '-path-data',
str(data), '-path-out',
str(out), '-script', dummy_script
])
def test_config_with_args_warning(tmp_path, dummy_script):
"""
Test that an error is thrown when trying to pass an argument ('-include') alongside a config file.
"""
data = tmp_path / 'data'
data.mkdir()
out = tmp_path / 'out'
config_path = tmp_path / 'config.json'
with open(config_path, 'w') as f:
config = {"jobs": 1, "path_data": str(data), "path_output": str(out)}
json.dump(config, f)
with pytest.warns(UserWarning, match=r'-config.*discouraged'):
sct_run_batch.main([
'-c',
str(config_path), '-include', 'something', '-script', dummy_script
])
def test_no_sessions(tmp_path, dummy_script):
"""
Test that individual subjects (i.e. not in 'ses' subfolders) can be processed individually by sct_run_batch.
"""
data = tmp_path / 'data'
data.mkdir()
out = tmp_path / 'out'
# Create dummy BIDS directory without sessions
for sub in ['01', '02']:
(data / f'sub-{sub}' / 'anat').mkdir(parents=True)
sct_run_batch.main([
'-path-data',
str(data), '-path-out',
str(out), '-script', dummy_script
])
for sub in ['01', '02']:
file_log = glob.glob(os.path.join(out, 'log', f'*sub-{sub}.log'))[0]
assert f'sub-{sub}' in open(file_log, "r").read()
def test_config_with_args_warning():
# This is formatted strangely because pep8 says so.
with \
NamedTemporaryFile('w', suffix='.json') as config,\
TemporaryDirectory() as data,\
TemporaryDirectory() as out:
cnf_text = '{{"jobs": 1, "path_data": "{}", "path_output": "{}"}}'.format(
data, out)
config.write(cnf_text)
config.flush()
with pytest.warns(UserWarning, match=r'-config.*discouraged'):
# I'm not sure how to check that argparse is printing the right error here, but I trust
with pytest.raises(FileNotFoundError):
sct_run_batch.main([
'-c', config.name, '-include', 'something', '-script',
'script'
])
def test_non_executable_task():
data_path = sct_test_path()
with \
NamedTemporaryFile('w', suffix='.sh') as script,\
TemporaryDirectory() as out:
script_text = """
#!/bin/bash
echo $SUBJECT
"""
script.write(
dedent(script_text)[1:]) #indexing removes beginning newline
script.flush()
assert not os.access(script.name, os.X_OK), "Script already executable"
sct_run_batch.main([
'-include', '^t.*', '-subject-prefix', '', '-path-data', data_path,
'-path-out', out, '-script', script.name, '-continue-on-error', 0
])
def test_config_extra_value_warning():
# This is formatted strangely because pep8 says so.
with \
NamedTemporaryFile('w', suffix='.yml') as config,\
TemporaryDirectory() as data,\
TemporaryDirectory() as out:
cnf_text = """
jobs: 1
path_data: {}
path_output: {}
unknowable: unknown
""".format(data, out)
config.write(dedent(cnf_text))
config.flush()
with pytest.warns(UserWarning, match='unknowable'):
# I'm not sure how to check that argparse is printing the right error here, but I trust
with pytest.raises(FileNotFoundError):
sct_run_batch.main(['-c', config.name, '-script', 'script'])
def test_config_extra_value_warning(tmp_path, dummy_script):
"""
Test that an error is thrown for passing a non-existent argument within a config file.
"""
data = tmp_path / 'data'
data.mkdir()
out = tmp_path / 'out'
config_path = str(tmp_path / 'config.yml')
with open(config_path, 'w') as config:
cnf_text = """
jobs: 1
path_data: {}
path_output: {}
unknowable: unknown
""".format(data, out)
config.write(dedent(cnf_text))
config.flush()
with pytest.warns(UserWarning, match='unknowable'):
sct_run_batch.main(['-c', config_path, '-script', dummy_script])
def test_non_executable_task(tmp_path, dummy_script):
"""
Test that sct_run_batch can still process a non-executable script. (sct_run_batch will attempt
to set the execute bit if passed a non-executable script.)
"""
data = tmp_path / 'data'
data.mkdir()
out = tmp_path / 'out'
# Set "Owner has execute permission" bit to 0 to ensure script is non-executable
script_stat = os.stat(dummy_script)
os.chmod(dummy_script, script_stat.st_mode & ~S_IEXEC)
# NB: This does nothing on Windows. (https://docs.python.org/3/library/os.html#os.chmod)
# > Although Windows supports chmod(), you can only set the file’s read-only flag with it
# > (via the stat.S_IWRITE and stat.S_IREAD constants or a corresponding integer value).
# > All other bits are ignored.
sct_run_batch.main([
'-include', '^t.*', '-subject-prefix', '', '-path-data',
str(data), '-path-out',
str(out), '-script', dummy_script, '-continue-on-error', 0
])
def test_separate_sessions(tmp_path, dummy_script):
"""
Test that sessions ('ses') can be separated so that sct_run_batch can process each session folder separately.
"""
data = tmp_path / 'data'
data.mkdir()
out = tmp_path / 'out'
# Create dummy BIDS directory with sessions
sub_ses_pairs = [('01', '01'), ('01', '02'), ('01', '03'), ('02', '01'),
('02', '02')]
for sub, ses in sub_ses_pairs:
(data / f'sub-{sub}' / f'ses-{ses}').mkdir(parents=True)
sct_run_batch.main([
'-path-data',
str(data), '-path-out',
str(out), '-script', dummy_script
])
for sub, ses in sub_ses_pairs:
file_log = glob.glob(
os.path.join(out, 'log', f'*sub-{sub}_ses-{ses}.log'))[0]
assert os.path.join(f'sub-{sub}', f'ses-{ses}') in open(file_log,
"r").read()