def test_context_dir():
with tempdir() as d1:
with context_dir(d1 / "foo") as d2:
foo = d2 / "foo"
with open(foo, "wt") as out:
out.write("foo")
assert foo.exists()
with context_dir() as d3:
bar = d3 / "bar"
with open(bar, "wt") as out:
out.write("bar")
assert not bar.exists()
d4 = d1 / "blorf"
assert not d4.exists()
with context_dir(d4):
assert d4.exists()
with context_dir(d4, cleanup=True):
pass
assert not d4.exists()
assert not foo.exists()
def _run_test(_executor_name):
executor = create_executor(_executor_name, import_dir_paths,
user_config)
with context_dir(user_config.default_execution_dir,
change_dir=True):
executor.run_workflow(wdl_path,
inputs=inputs,
expected=expected,
**kwargs)
def _run_workflow(wdl_script: Union[str, Path],
workflow_name: Optional[str] = None,
inputs: Optional[dict] = None,
expected: Optional[dict] = None,
executor_name: str = "cromwell",
**kwargs):
executor_class = EXECUTORS.get(executor_name)
if not executor_class:
raise RuntimeError(
f"{executor_name} executor plugin is not installed")
executor = executor_class(
project_root=project_root,
import_dirs=import_dirs,
**user_config.get_executor_defaults(executor_name))
with context_dir(user_config.default_execution_dir, change_dir=True):
executor.run_workflow(wdl_script, workflow_name, inputs, expected,
**kwargs)
def _run_test(self,
executor_name: str,
wdl_path: Path,
inputs: Optional[dict] = None,
expected: Optional[dict] = None,
callback: Optional[Callable[[str, Path, dict], None]] = None,
**kwargs) -> dict:
executor = create_executor(executor_name, self._import_dirs,
self._user_config)
with context_dir(self._user_config.default_execution_dir,
change_dir=True) as execution_dir:
outputs = executor.run_workflow(wdl_path,
inputs=inputs,
expected=expected,
**kwargs)
if callback:
callback(executor_name, execution_dir, outputs)
return outputs