def __init__(self, args: argparse.Namespace):
self.env = Env()
arg_dict = vars(args)
for arg in arg_dict:
arg_val = arg_dict.get(arg)
if isinstance(arg_val, Path):
arg_val = arg_val.resolve()
setattr(self, arg, arg_val)
def test_load_env_from_file(env_inst: Env):
env_inst.set_env("TEST", "TEST")
env_inst.save()
env_inst.reset()
assert not env_inst.env
env_inst.load_env_from_file()
assert env_inst.env
def test_load_env_to_os(env_inst: Env):
env_key = "CWAS_TEST"
env_value = "HELLO"
env_inst.set_env(env_key, env_value)
env_inst.save()
env_inst.load_env_to_os()
assert os.getenv(env_key) == env_value
env_inst.get_path().unlink()
os.environ.pop(env_key)
def test_env_singleton(cwas_env_path: Path):
env1 = Env()
env2 = Env()
assert env1 is env2
new_env_path = Path(str(cwas_env_path) + "_new")
env3 = Env(new_env_path)
env4 = Env()
assert env1 is env3
assert env1 is env4
assert env1.get_path() is new_env_path
env1.set_path(cwas_env_path)
def teardown(cwas_workspace):
yield
env = Env()
env.reset()
env.remove_file()
for f in cwas_workspace.glob("*"):
f.unlink()
cwas_workspace.rmdir()
def teardown(cwas_workspace: Path, vep_mock: Path):
yield
vep_mock.unlink()
env = Env()
env.reset()
env.remove_file()
for f in cwas_workspace.glob("*"):
f.unlink()
cwas_workspace.rmdir()
def test_env_save(env_inst: Env):
env_key = "TEST"
expected = "Hello!"
env_inst.set_env(env_key, expected)
env_inst.save()
cwas_env_path = env_inst.get_path()
with cwas_env_path.open() as env_file:
env_line = env_file.read()
env_line = env_line.strip()
assert env_line == "TEST=Hello!"
env_inst.get_path().unlink()
class Runnable(ABC):
def __init__(self, args: argparse.Namespace):
self.env = Env()
arg_dict = vars(args)
for arg in arg_dict:
arg_val = arg_dict.get(arg)
if isinstance(arg_val, Path):
arg_val = arg_val.resolve()
setattr(self, arg, arg_val)
@classmethod
def get_instance(cls, argv: list = []) -> Runnable:
arg_parser = cls._create_arg_parser()
args = arg_parser.parse_args(argv)
cls._print_args(args)
cls._check_args_validity(args)
return cls(args)
def set_env_path(self, path: Path):
self.env.set_path(path)
def set_env(self, env_key: str, env_value: Any):
self.env.set_env(env_key, env_value)
def get_env(self, env_key: str) -> Optional[str]:
return self.env.get_env(env_key)
def save_env(self):
self.env.save()
@staticmethod
def _create_arg_parser() -> argparse.ArgumentParser:
return argparse.ArgumentParser()
@staticmethod
def _print_args(args: argparse.Namespace):
pass
@staticmethod
def _check_args_validity(args: argparse.Namespace):
pass
@abstractmethod
def run(self):
pass
def test_env_prev_set_exists(env_inst: Env):
# Test if the environment variable exists.
env_key = "TEST"
expected = "Hello!"
env_value = env_inst.get_env(env_key)
assert env_value == expected
def test_env_reset(env_inst: Env):
env_inst.reset()
env_key = "TEST"
env_value = env_inst.get_env(env_key)
assert not env_inst.env
assert env_value is None
def test_env_setting(env_inst: Env):
env_key = "TEST"
expected = "Hello!"
env_inst.set_env(env_key, expected)
env_value = env_inst.get_env(env_key)
assert env_value == expected
def test_env_get_nonexist(env_inst: Env):
env_value = env_inst.get_env("FAKE")
assert env_value is None
def test_env_init(env_inst: Env, cwas_env_path: Path):
assert env_inst.get_path() is cwas_env_path
assert isinstance(env_inst.env, OrderedDict)
def set_env(cwas_workspace: Path):
env = Env()
env.set_env("CWAS_WORKSPACE", cwas_workspace)
env.save()
def set_env(cwas_workspace, annotation_dir):
env = Env()
env.set_env("CWAS_WORKSPACE", cwas_workspace)
env.set_env("VEP", "VEP")
env.set_env("ANNOTATION_DATA", annotation_dir)
env.set_env("ANNOTATION_BW_KEY", annotation_dir / "bw_key.yaml")
env.set_env("MERGED_BED", cwas_workspace / "merged.bed.gz")
env.set_env("MERGED_BED_INDEX", cwas_workspace / "merged.bed.gz.tbi")
env.save()
def test_run_without_configuration():
inst = PreparationMock.get_instance()
Env().reset()
with pytest.raises(RuntimeError):
inst.run()
def set_env(cwas_workspace: Path, annotation_dir: Path):
env = Env()
env.set_env("CWAS_WORKSPACE", cwas_workspace)
env.set_env("ANNOTATION_DATA", annotation_dir)
env.set_env("ANNOTATION_BED_KEY", cwas_workspace / "bed_key.yaml")
env.save()
def test_load_env_to_os_without_save(env_inst: Env):
env_key = "CWAS_TEST"
env_value = "HELLO"
env_inst.set_env(env_key, env_value)
env_inst.load_env_to_os()
assert os.getenv(env_key) is None
def reset_env():
env = Env()
env.reset()
env.remove_file()
def env_inst():
return Env()
def teardown(env_inst: Env):
yield
env_inst.reset()
env_inst.remove_file()
def cwas_env_inst(cwas_env_path):
env_inst = Env(cwas_env_path)
yield
env_inst.remove_file()
def _make_env_empty():
env = Env()
env.reset()
env.save()