Merge pull request #18535 from mvdbeek/runtime_input_map_over_fix (4de96cc4) · Commits · NDIP / Galaxy

lib/galaxy/tools/parameters/wrapped.py

+30 −1

Original line number	Diff line number	Diff line
		@@ -3,6 +3,8 @@ from typing import (
		Any,
		Dict,
		List,
		Sequence,
		Union,
		)

		from galaxy.tools.parameters.basic import (
		@@ -187,6 +189,26 @@ def process_key(incoming_key: str, incoming_value: Any, d: Dict[str, Any]):
		process_key("\|".join(key_parts[1:]), incoming_value=incoming_value, d=subdict)


		def nested_key_to_path(key: str) -> Sequence[Union[str, int]]:
		"""
		Convert a tool state key that is separated with '\|' and '_n' into path iterable.
		E.g. "cond\|repeat_0\|paramA" -> ["cond", "repeat", 0, "paramA"].
		Return value can be used with `boltons.iterutils.get_path`.
		"""
		path: List[Union[str, int]] = []
		key_parts = key.split("\|")
		if len(key_parts) == 1:
		return key_parts
		for key_part in key_parts:
		if "_" in key_part:
		input_name, _index = key_part.rsplit("_", 1)
		if _index.isdigit():
		path.extend((input_name, int(_index)))
		continue
		path.append(key_part)
		return path


		def flat_to_nested_state(incoming: Dict[str, Any]):
		nested_state: Dict[str, Any] = {}
		for key, value in incoming.items():
		@@ -194,4 +216,11 @@ def flat_to_nested_state(incoming: Dict[str, Any]):
		return nested_state


		__all__ = ("LegacyUnprefixedDict", "WrappedParameters", "make_dict_copy", "process_key", "flat_to_nested_state")
		__all__ = (
		"LegacyUnprefixedDict",
		"WrappedParameters",
		"make_dict_copy",
		"process_key",
		"flat_to_nested_state",
		"nested_key_to_path",
		)

+6 −0

Original line number	Diff line number	Diff line
		@@ -10,6 +10,7 @@ from typing import (
		Union,
		)

		from boltons.iterutils import get_path
		from typing_extensions import Protocol

		from galaxy import model
		@@ -35,6 +36,7 @@ from galaxy.schema.invocation import (
		WarningReason,
		)
		from galaxy.tools.parameters.basic import raw_to_galaxy
		from galaxy.tools.parameters.wrapped import nested_key_to_path
		from galaxy.util import ExecutionTimer
		from galaxy.workflow import modules
		from galaxy.workflow.run_request import (
		@@ -444,6 +446,10 @@ class WorkflowProgress:
		replacement = temp
		else:
		replacement = self.replacement_for_connection(connection[0], is_data=is_data)
		elif step.state and (state_input := get_path(step.state.inputs, nested_key_to_path(prefixed_name), None)):
		# workflow submitted with step parameters populates state directly
		# via populate_module_and_state
		replacement = state_input
		else:
		for step_input in step.inputs:
		if step_input.name == prefixed_name and step_input.default_value_set:

+29 −0

Original line number	Diff line number	Diff line
		@@ -6982,6 +6982,35 @@ steps:
		# Take a valid stat and make it invalid, assert workflow won't run.
		self._assert_status_code_is(invocation_response, 400)

		@skip_without_tool("collection_paired_test")
		def test_run_map_over_with_step_parameter_dict(self):
		# Tests what the legacy run form submits
		with self.dataset_populator.test_history() as history_id:
		hdca = self.dataset_collection_populator.create_list_of_pairs_in_history(history_id).json()["outputs"][0]
		workflow_id = self._upload_yaml_workflow(
		"""
		class: GalaxyWorkflow
		steps:
		"0":
		tool_id: collection_paired_conditional_structured_like
		state:
		cond:
		input1:
		__class__: RuntimeValue
		"""
		)
		workflow_request = {
		"history": f"hist_id={history_id}",
		"parameters": dumps({"0": {"cond\|input1": {"values": [{"id": hdca["id"], "src": "hdca"}]}}}),
		"parameters_normalized": True,
		}
		url = f"workflows/{workflow_id}/invocations"
		invocation_response = self._post(url, data=workflow_request, json=True)
		invocation_response.raise_for_status()
		self.workflow_populator.wait_for_invocation_and_jobs(
		history_id=history_id, workflow_id=workflow_id, invocation_id=invocation_response.json()["id"]
		)

		@skip_without_tool("validation_default")
		def test_parameter_substitution_validation_value_errors_1(self):
		substitions = dict(select_param='" ; echo "moo')

+19 −1

Original line number	Diff line number	Diff line
		@@ -3,10 +3,28 @@ from typing import (
		Dict,
		)

		from galaxy.tools.parameters.wrapped import process_key
		from galaxy.tools.parameters.wrapped import (
		nested_key_to_path,
		process_key,
		)
		from .util import BaseParameterTestCase


		def test_nested_key_to_path():
		assert nested_key_to_path("param") == ["param"]
		assert nested_key_to_path("param_x") == ["param_x"]
		assert nested_key_to_path("cond\|param_x") == ["cond", "param_x"]
		assert nested_key_to_path("param_") == ["param_"]
		assert nested_key_to_path("cond\|param_") == ["cond", "param_"]
		assert nested_key_to_path("repeat_1\|inner_repeat_1\|data_table_column_value") == [
		"repeat",
		1,
		"inner_repeat",
		1,
		"data_table_column_value",
		]


		class TestProcessKey:
		def test_process_key(self):
		nested_dict: Dict[str, Any] = {}