From ff2309156eba2e18f4eddd945184730964b827ee Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 11 Jul 2024 16:45:50 +0200
Subject: [PATCH] Fix map over calculation for runtime inputs

Fixes https://github.com/galaxyproject/galaxy/issues/18506
---
 lib/galaxy/tools/parameters/wrapped.py        | 31 ++++++++++++++++++-
 lib/galaxy/workflow/run.py                    |  6 ++++
 test/unit/app/tools/test_parameter_parsing.py | 20 +++++++++++-
 3 files changed, 55 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tools/parameters/wrapped.py b/lib/galaxy/tools/parameters/wrapped.py
index dbcc4d1f0a03..c269088f8b84 100644
--- a/lib/galaxy/tools/parameters/wrapped.py
+++ b/lib/galaxy/tools/parameters/wrapped.py
@@ -3,6 +3,8 @@
     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 = []
+    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",
+)
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index ebc1bdf5ffe9..9eb3be3c9dae 100644
--- a/lib/galaxy/workflow/run.py
+++ b/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))):
+            # 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:
diff --git a/test/unit/app/tools/test_parameter_parsing.py b/test/unit/app/tools/test_parameter_parsing.py
index 28d7565ff1a8..842e7df91844 100644
--- a/test/unit/app/tools/test_parameter_parsing.py
+++ b/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] = {}