Fix path resolution for composite test data upload (eb95601f) · Commits · NDIP / Galaxy

lib/galaxy/tool_util/verify/interactor.py

+61 −26

Original line number	Diff line number	Diff line
		@@ -138,6 +138,12 @@ ToolTestDict = Union[ValidToolTestDict, InvalidToolTestDict]
		ToolTestDictsT = List[ToolTestDict]


		class PathOrLocation(NamedTuple):
		name: str
		path: Optional[str]
		location: Optional[str]


		def stage_data_in_history(
		galaxy_interactor: "GalaxyInteractorApi",
		tool_id: str,
		@@ -560,8 +566,41 @@ class GalaxyInteractorApi:

		composite_data = test_data["composite_data"]
		if composite_data:
		tool_input["composite_data"] = composite_data
		tool_input["composite_data"] = [
		self._get_path_or_location(
		fname=fname_,
		test_data={},
		tool_id=tool_id,
		tool_version=tool_version,
		force_path_paste=force_path_paste,
		).path
		for fname_ in composite_data
		]
		else:
		assert fname, "File path is required and cannot be empty string"
		path_or_location = self._get_path_or_location(
		fname,
		test_data,
		tool_id,
		tool_version=tool_version,
		mode="file" if tool_input["class"].lower() == "file" else "directory",
		)
		if path_or_location.path:
		tool_input["path"] = path_or_location.path
		if path_or_location.location:
		tool_input["location"] = path_or_location.location
		tool_input["name"] = os.path.basename(path_or_location.name)
		return tool_input

		def _get_path_or_location(
		self,
		fname: str,
		test_data: Dict[str, Any],
		tool_id: str,
		tool_version: Optional[str] = None,
		force_path_paste: bool = False,
		mode: Literal["file", "directory"] = "file",
		) -> PathOrLocation:
		file_name = None
		file_name_exists = False
		location = self._ensure_valid_location_in(test_data)
		@@ -569,25 +608,21 @@ class GalaxyInteractorApi:
		file_name = self.test_data_path(tool_id, fname, tool_version=tool_version)
		file_name_exists = os.path.exists(file_name)
		if not file_name_exists and location is not None:
		name = location
		tool_input["location"] = location
		return PathOrLocation(name=location, location=location, path=None)
		else:
		name = fname
		if force_path_paste:
		if file_name is None:
		file_name = self.test_data_path(tool_id, fname, tool_version=tool_version)
		tool_input["location"] = f"file://{file_name}"
		return PathOrLocation(name=fname, location=f"file://{file_name}", path=None)
		else:
		mode = "file" if tool_input["class"].lower() == "file" else "directory"
		tool_input["path"] = path = self.test_data_download(
		path = self.test_data_download(
		tool_id, fname, is_output=False, tool_version=tool_version, mode=mode, path_only=True
		)
		assert isinstance(path, str)
		# Downloaded directories contain root directory
		if path and mode == "directory":
		tool_input["path"] = path if mode == "file" else os.path.join(path, fname)
		name = os.path.basename(name)
		tool_input["name"] = name
		return tool_input
		path = os.path.join(path, fname)
		return PathOrLocation(name=fname, location=None, path=path)

		def _ensure_valid_location_in(self, test_data: dict) -> Optional[str]:
		location: Optional[str] = test_data.get("location")

lib/galaxy/tool_util/verify/parse.py

+3 −1

Original line number	Diff line number	Diff line
		@@ -533,7 +533,9 @@ def _add_uploaded_dataset(
		required_files: RequiredFilesT,
		) -> Optional[str]:
		if value is None:
		assert input_parameter.parse_optional(), f"{name} is not optional. You must provide a valid filename."
		assert (
		input_parameter.parse_optional() or "composite_data" in extra
		), f"{name} is not optional. You must provide a valid filename."
		return value
		return require_file(name, value, extra, required_files)