Fix tool request API for multiple select parameters with defaults.

lib/galaxy/tool_util/parameters/convert.py

@@ -289,7 +289,7 @@ def encode_test(
                 test_collection = cast(JsonTestCollectionDefDict, value)
                 return adapt_collections(test_collection).model_dump()
         elif isinstance(parameter, SelectParameterModel):
-            if parameter.multiple and value is not None:
+            if parameter.multiple and value is not None and isinstance(value, (str,)):
                 return [v.strip() for v in value.split(",")]
             else:
                 return VISITOR_NO_REPLACEMENT
@@ -359,7 +359,7 @@ def _fill_default_for(tool_state: Dict[str, Any], parameter: ToolParameterT) ->
             if not parameter.multiple:
                 tool_state[parameter_name] = parameter.default_value
             else:
-                tool_state[parameter_name] = None
+                tool_state[parameter_name] = parameter.default_values
     elif isinstance(parameter, DrillDownParameterModel):
         if parameter_name not in tool_state:
             if parameter.multiple:

lib/galaxy/tool_util_models/parameters.py

@@ -1175,6 +1175,7 @@ class SelectParameterModel(BaseGalaxyToolParameterModelDefinition):
 
     @property
     def default_value(self) -> Optional[str]:
+        assert not self.multiple
         if self.options:
             for option in self.options:
                 if option.selected:
@@ -1185,6 +1186,13 @@ class SelectParameterModel(BaseGalaxyToolParameterModelDefinition):
 
         return None
 
+    @property
+    def default_values(self) -> Optional[List[str]]:
+        assert self.multiple
+        if self.options:
+            return [option.value for option in self.options if option.selected]
+        return None
+
     @property
     def request_requires_value(self) -> bool:
         # API will allow an empty value and just grab the first static option

lib/galaxy_test/api/test_tool_execute.py

@@ -681,6 +681,17 @@ def test_select_multiple_does_not_select_first_by_default(
         ).with_contents_stripped("None")
 
 
+@requires_tool_id("gx_select_multiple_one_default")
+def test_select_multiple_does_default_to_select_values_marked_as_selected(
+    required_tools: list[RequiredTool], tool_input_format: DescribeToolInputs
+):
+    empty = tool_input_format.when.any({})
+    for required_tool in required_tools:
+        required_tool.execute.with_inputs(empty).assert_has_single_job.with_output("output").with_contents_stripped(
+            "--ex3"
+        )
+
+
 @requires_tool_id("gx_text")
 @requires_tool_id("gx_text_optional_false")
 def test_null_to_text_tools(required_tools: list[RequiredTool], tool_input_format: DescribeToolInputs):

test/functional/tools/parameters/gx_select_multiple_one_default.xml

@@ -0,0 +1,35 @@
+<tool id="gx_select_multiple_one_default" name="gx_select_multiple_one_default" version="1.0.0">
+    <command><![CDATA[
+echo '$parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="parameter" type="select" multiple="true">
+            <option value="--ex1">Ex1</option>
+            <option value="ex2">Ex2</option>
+            <option value="--ex3" selected="true">Ex3</option>
+            <option value="--ex4">Ex4</option>
+            <option value="ex5">Ex5</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="parameter" value="ex2" />
+            <output name="output">
+                <assert_contents>
+                    <has_line line="ex2" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <!-- these parameters are not implicitly optional and don't select top option -->
+            <output name="output">
+                <assert_contents>
+                    <has_line line="--ex3" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>

test/functional/tools/simple_constructs.xml

@@ -59,6 +59,7 @@ echo $drop_select  >> '$out_file1' &&
                     <has_line line="booltrue" />
                     <has_line line="12456" />
                     <has_line line="6.789" />
+                    <has_line line="a_check" />
                     <has_line line="This is a line of text." />
                 </assert_contents>
             </output>

test/unit/tool_util/test_parameter_convert.py

@@ -232,12 +232,14 @@ def test_fill_defaults():
     with_defaults = fill_state_for({}, "parameters/gx_select_optional")
     assert with_defaults["parameter"] is None
 
-    # Not ideal but matching current behavior
     with_defaults = fill_state_for({}, "parameters/gx_select_multiple")
-    assert with_defaults["parameter"] is None
+    assert with_defaults["parameter"] == []
 
     with_defaults = fill_state_for({}, "parameters/gx_select_multiple_optional")
-    assert with_defaults["parameter"] is None
+    assert with_defaults["parameter"] == []
+
+    with_defaults = fill_state_for({}, "parameters/gx_select_multiple_one_default")
+    assert with_defaults["parameter"] == ["--ex3"]
 
     # Do not fill in dynamic defaults... these require a Galaxy runtime.
     with_defaults = fill_state_for({}, "remove_value", partial=True)