Stop exposing flat nested inputs in workflow when expressions

doc/source/releases/26.2_announce.rst

@@ -4,3 +4,12 @@
 ===========================================================
 26.2 Galaxy Release
 ===========================================================
+
+Workflow expression compatibility
+=================================
+
+Workflow ``when`` expressions no longer expose connected nested tool inputs
+through Galaxy's internal pipe-prefixed connection names (for example,
+``inputs["cond|param"]``). Use the nested tool-state form instead, such as
+``inputs.cond.param`` or ``inputs["cond"]["param"]``. Ordinary top-level inputs
+and extra expression inputs such as ``inputs.when`` remain unchanged.

lib/galaxy/workflow/modules.py

@@ -3117,25 +3117,23 @@ class ToolModule(WorkflowModule):
                 extra_step_state = {}
                 for step_input in step.inputs:
                     step_input_name = step_input.name
-                    input_in_execution_state = step_input_name not in execution_state.inputs
-                    if input_in_execution_state:
-                        if step_input_name in all_inputs_by_name:
-                            if iteration_elements and step_input_name in iteration_elements:  # noqa: B023
-                                value = iteration_elements[step_input_name]  # noqa: B023
-                            else:
-                                value = progress.replacement_for_input(trans, step, all_inputs_by_name[step_input_name])
-                            # TODO: only do this for values... is everything with a default
-                            # this way a field parameter? I guess not?
-                            extra_step_state[step_input_name] = value
-                        # Might be needed someday...
-                        # elif step_input.default_value_set:
-                        #    extra_step_state[step_input_name] = step_input.default_value
+                    if step_input_name in execution_state.inputs:
+                        continue
+                    if step_input_name in all_inputs_by_name:
+                        if step_input_name and "|" in step_input_name:
+                            # Nested tool inputs have flat connection names but are already represented
+                            # by their nested shape in the execution state.
+                            continue
+                        if iteration_elements and step_input_name in iteration_elements:  # noqa: B023
+                            value = iteration_elements[step_input_name]  # noqa: B023
                         else:
-                            if iteration_elements and step_input_name in iteration_elements:  # noqa: B023
-                                value = iteration_elements[step_input_name]  # noqa: B023
-                            else:
-                                value = progress.replacement_for_connection(step_input.connections[0], is_data=True)
-                            extra_step_state[step_input_name] = value
+                            value = progress.replacement_for_input(trans, step, all_inputs_by_name[step_input_name])
+                    else:
+                        if iteration_elements and step_input_name in iteration_elements:  # noqa: B023
+                            value = iteration_elements[step_input_name]  # noqa: B023
+                        else:
+                            value = progress.replacement_for_connection(step_input.connections[0], is_data=True)
+                    extra_step_state[step_input_name] = value
 
                 if when_value is not False:
                     when_value = evaluate_value_from_expressions(

lib/galaxy_test/workflow/when_expression_nested_tool_inputs.gxwf-tests.yml

@@ -0,0 +1,16 @@
+- doc: Nested dot and bracket access work when an optional input is omitted.
+  job: {}
+  outputs:
+    out:
+      asserts:
+        has_line:
+          line: okay
+- doc: Nested dot and bracket access work when an optional input is supplied.
+  job:
+    optional_text: supplied
+    expected: supplied
+  outputs:
+    out:
+      asserts:
+        has_line:
+          line: okay

lib/galaxy_test/workflow/when_expression_nested_tool_inputs.gxwf.yml

@@ -0,0 +1,31 @@
+class: GalaxyWorkflow
+doc: |
+  Ensure workflow when expressions expose connected tool parameters only in
+  their tool-state shape while preserving genuine extra expression inputs.
+inputs:
+  optional_text:
+    type: text
+    optional: true
+  gate:
+    type: boolean
+    default: true
+  expected:
+    type: text
+    default: fdefault
+outputs:
+  out:
+    outputSource: inputs_as_json/out_file1
+steps:
+  inputs_as_json:
+    tool_id: inputs_as_json
+    state:
+      test_case: 0
+      cond:
+        cond_test: first
+    in:
+      cond|more_text: optional_text
+      booltest: gate
+      when: gate
+      probe: gate
+      expected: expected
+    when: $(inputs.when && inputs.probe && inputs.booltest === inputs["booltest"] && inputs.cond.more_text === inputs["cond"]["more_text"] && inputs.cond.more_text === inputs.expected && !("cond|more_text" in inputs))