[24.1] Fix map over calculation for runtime inputs

lib/galaxy/tools/parameters/wrapped.py

@@ -3,6 +3,8 @@
     Any,
     Dict,
     List,
+    Sequence,
+    Union,
 )
 
 from galaxy.tools.parameters.basic import (
@@ -187,11 +189,38 @@ 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():
         process_key(key, value, nested_state)
     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",
+)

lib/galaxy/workflow/run.py

@@ -10,6 +10,7 @@
     Union,
 )
 
+from boltons.iterutils import get_path
 from typing_extensions import Protocol
 
 from galaxy import model
@@ -35,6 +36,7 @@
     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 @@ def replacement_for_input(self, trans, step: "WorkflowStep", input_dict: Dict[st
                     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:

lib/galaxy_test/api/test_workflows.py

@@ -6982,6 +6982,35 @@ def test_parameter_substitution_validation_value_errors_0(self):
             # 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')

test/unit/app/tools/test_parameter_parsing.py

@@ -3,10 +3,28 @@
     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] = {}