Start to work on fixing up 21.01 parameters...

jmchilton · Oct 16, 2024 · 7640061 · 7640061
1 parent d04d462
commit 7640061
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Showing 3 changed files with 25 additions and 7 deletions.
diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py
@@ -454,10 +454,13 @@ def populate_state(
                         current_case = conditional_input.get_current_case(value)
                         group_state = state[conditional_input.name] = {}
                         cast_errors: ParameterValidationErrorsT = {}
+                        incoming_for_conditional = cast(
+                            ToolStateJobInstanceT, incoming.get(conditional_input.name) or {}
+                        )
                         populate_state(
                             request_context,
                             conditional_input.cases[current_case].inputs,
-                            cast(ToolStateJobInstanceT, incoming.get(conditional_input.name)),
+                            incoming_for_conditional,
                             group_state,
                             cast_errors,
                             context=context,
@@ -475,10 +478,11 @@ def populate_state(
             elif input.type == "section":
                 section_input = cast(Section, input)
                 section_errors: ParameterValidationErrorsT = {}
+                incoming_for_state = cast(ToolStateJobInstanceT, incoming.get(section_input.name) or {})
                 populate_state(
                     request_context,
                     section_input.inputs,
-                    cast(ToolStateJobInstanceT, incoming.get(section_input.name)),
+                    incoming_for_state,
                     group_state,
                     section_errors,
                     context=context,

diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py
@@ -802,6 +802,8 @@ def __init__(self, input_datasets: Optional[Dict[str, Any]] = None) -> None:
             self.identifier_key_dict = {}
 
     def identifier(self, dataset_value: str, input_values: Dict[str, str]) -> Optional[str]:
+        if isinstance(dataset_value, list):
+            raise TypeError(f"Expected {dataset_value} to be hashable")
         element_identifier = None
         if identifier_key := self.identifier_key_dict.get(dataset_value, None):
             element_identifier = input_values.get(identifier_key, None)

diff --git a/lib/galaxy_test/api/test_tool_execute.py b/lib/galaxy_test/api/test_tool_execute.py
@@ -87,9 +87,11 @@ def test_identifier_map_over_multiple_input_in_conditional(
     target_history: TargetHistory, required_tool: RequiredTool, tool_input_format: DescribeToolInputs
 ):
     hdca = target_history.with_pair()
-    inputs = tool_input_format.when.flat({
-        "outer_cond|input1": hdca.src_dict,
-    }).when.nested(
+    inputs = tool_input_format.when.flat(
+        {
+            "outer_cond|input1": hdca.src_dict,
+        }
+    ).when.nested(
         {
             "outer_cond": {
                 "multi_input": True,
@@ -115,15 +117,25 @@ def test_identifier_multiple_reduce_in_repeat_new_payload_form(
 
 
 @requires_tool_id("output_action_change_format")
-def test_map_over_with_output_format_actions(target_history: TargetHistory, required_tool: RequiredTool):
+def test_map_over_with_output_format_actions(
+    target_history: TargetHistory, required_tool: RequiredTool, tool_input_format: DescribeToolInputs
+):
     hdca = target_history.with_pair()
     for use_action in ["do", "dont"]:
-        execute = required_tool.execute.with_inputs(
+        inputs = tool_input_format.when.flat(
             {
                 "input_cond|dispatch": use_action,
                 "input_cond|input": {"batch": True, "values": [hdca.src_dict]},
             }
+        ).when.nested(
+            {
+                "input_cond": {
+                    "dispatch": use_action,
+                    "input": {"batch": True, "values": [hdca.src_dict]},
+                }
+            }
         )
+        execute = required_tool.execute.with_inputs(inputs)
         execute.assert_has_n_jobs(2).assert_creates_n_implicit_collections(1)
         expected_extension = "txt" if (use_action == "do") else "data"
         execute.assert_has_job(0).with_single_output.with_file_ext(expected_extension)