def get_workflow(project_root: Path,
wdl_file: Union[str, Path],
workflow_name: Optional[str] = None) -> Tuple[Path, str]:
"""
Resolve the WDL file and workflow name.
TODO: if `workflow_name` is None, parse the WDL file and extract the name
of the workflow.
Args:
project_root: The root directory to which `wdl_file` might be relative.
wdl_file: Path to the WDL file.
workflow_name: The workflow name; if None, the filename without ".wdl"
extension is used.
Returns:
A tuple (wdl_path, workflow_name)
"""
wdl_path = ensure_path(wdl_file, project_root, canonicalize=True)
if not wdl_path.exists():
raise FileNotFoundError(f"WDL file not found at path {wdl_path}")
if not workflow_name:
workflow_name = safe_string(wdl_path.stem)
return wdl_path, workflow_name
def get_target_name(wdl_path: Optional[Path] = None,
wdl_doc: Optional[Document] = None,
task_name: Optional[str] = None,
workflow_name: Optional[str] = None,
**kwargs) -> Tuple[str, bool]:
"""
Get the execution target. The order of priority is:
- task_name
- workflow_name
- wdl_doc.workflow.name
- wdl_doc.task[0].name
- wdl_file.stem
Args:
wdl_path: Path to a WDL file
wdl_doc: A miniwdl-parsed WDL document
task_name: The task name
workflow_name: The workflow name
**kwargs: Additional keyword arguments to pass to `parse_wdl`
Returns:
A tuple (target, is_task), where `is_task` is a boolean indicating whether
the target is a task (True) or a workflow (False).
Raises:
ValueError if 1) neither `task_name` nor `workflow_name` is specified and the
WDL document contains no workflow and multiple tasks; or 2) all of the
parameters are None.
"""
if task_name:
return task_name, True
if workflow_name:
return workflow_name, False
if not wdl_doc and Tree:
wdl_doc = parse_wdl(wdl_path, **kwargs)
if wdl_doc:
if wdl_doc.workflow:
return wdl_doc.workflow.name, False
elif wdl_doc.tasks and len(wdl_doc.tasks) == 1:
return wdl_doc.tasks[0].name, True
else:
raise ValueError(
"WDL document has no workflow and multiple tasks, and 'task_name' "
"is not specified")
if wdl_path:
return safe_string(wdl_path.stem), False
raise ValueError("At least one parameter must not be None")
def _get_workflow_name(self, wdl_path: Path, kwargs: dict):
if "workflow_name" in kwargs:
return kwargs["workflow_name"]
elif Tree:
if "check_quant" not in kwargs:
kwargs["check_quant"] = False
doc = Tree.load(str(wdl_path),
path=[str(path) for path in self.import_dirs],
**kwargs)
return doc.workflow.name
else: # TODO: test this
return safe_string(wdl_path.stem)
def test_safe_string():
assert safe_string("a+b*c") == "a_b_c"