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 __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 teardown(cwas_workspace):
yield
env = Env()
env.reset()
env.remove_file()
for f in cwas_workspace.glob("*"):
f.unlink()
cwas_workspace.rmdir()
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 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 cwas_env_inst(cwas_env_path):
env_inst = Env(cwas_env_path)
yield
env_inst.remove_file()
def env_inst():
return Env()
def reset_env():
env = Env()
env.reset()
env.remove_file()
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_run_without_configuration():
inst = PreparationMock.get_instance()
Env().reset()
with pytest.raises(RuntimeError):
inst.run()
def set_env(cwas_workspace: Path):
env = Env()
env.set_env("CWAS_WORKSPACE", cwas_workspace)
env.save()
def _make_env_empty():
env = Env()
env.reset()
env.save()