def test_EnvironmentError_raised_if_command_not_found(
self, mock_run, mock_env):
mock_run.return_value = (0, '')
with pytest.raises(EnvironmentError):
utils.check_dependency_configured('FreeSurfer',
shell_cmd='recon-all')
def test_EnvironmentError_raised_if_any_env_variable_not_defined(self, mock_env):
mock_env.__getitem__.side_effect = lambda x: self.fake_env[x]
variables = ['PATH', 'FREESURFER_HOME']
utils.check_dependency_configured('MyProgram', env_vars=variables)
assert False
def test_exits_successfully_when_command_path_found_and_vars_set(self,
mock_run, mock_env):
mock_env.__getitem__.side_effect = lambda x: self.fake_env[x]
cmd = 'fsl'
def which(name):
if name == 'which {}'.format(cmd):
return (0, '/some/path')
return (0, '')
mock_run.side_effect = which
variables = ['FSLDIR']
utils.check_dependency_configured('FSL', shell_cmd=cmd, env_vars=variables)
assert True
def check_environment():
try:
utils.check_dependency_configured('FSL', shell_cmd='fsl',
env_vars=['FSLDIR'])
utils.check_dependency_configured('FreeSurfer', shell_cmd='recon-all',
env_vars=['FREESURFER_HOME'])
utils.check_dependency_configured('Connectome-Workbench',
shell_cmd='wb_command')
utils.check_dependency_configured('HCP pipelines', env_vars=['HCPPIPEDIR',
'HCPPIPEDIR_Config', 'HCPPIPEDIR_FS', 'HCPPIPEDIR_Global',
'HCPPIPEDIR_PostFS', 'HCPPIPEDIR_PreFS', 'HCPPIPEDIR_Templates'])
except EnvironmentError as e:
logger.error(e.message)
sys.exit(1)
def test_doesnt_require_list_for_single_env_var(self, mock_env):
mock_env.__getitem__.side_effect = lambda x: self.fake_env[x]
utils.check_dependency_configured('SomeProgram', env_vars='PATH')
# If function exits without error, this test should always pass
assert True
def test_doesnt_require_list_for_single_env_var(self, mock_env):
mock_env.__getitem__.side_effect = lambda x: self.fake_env[x]
utils.check_dependency_configured('SomeProgram', env_vars='PATH')
# If function exits without error, this test should always pass
assert True
def test_EnvironmentError_raised_if_command_not_found(self, mock_run,
mock_env):
mock_run.return_value = (0, '')
utils.check_dependency_configured('FreeSurfer', shell_cmd='recon-all')
