Parameter models for optional data columns.

galaxyproject · Aug 10, 2024 · fcb0ebd · fcb0ebd
1 parent baee7f1
commit fcb0ebd
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Showing 4 changed files with 46 additions and 2 deletions.
diff --git a/lib/galaxy/tool_util/parameters/factory.py b/lib/galaxy/tool_util/parameters/factory.py
@@ -171,9 +171,11 @@ def _from_input_source_galaxy(input_source: InputSource) -> ToolParameterT:
             )
         elif param_type == "data_column":
             multiple = input_source.get_bool("multiple", False)
+            optional = input_source.parse_optional()
             return DataColumnParameterModel(
                 name=input_source.parse_name(),
                 multiple=multiple,
+                optional=optional,
             )
         elif param_type == "group_tag":
             multiple = input_source.get_bool("multiple", False)

diff --git a/lib/galaxy/tool_util/parameters/models.py b/lib/galaxy/tool_util/parameters/models.py
@@ -610,14 +610,14 @@ def py_type(self) -> Type:
         py_type: Type = StrictInt
         if self.multiple:
             py_type = list_type(py_type)
-        return py_type
+        return optional_if_needed(py_type, self.optional)
 
     def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
         return dynamic_model_information_from_py_type(self, self.py_type)
 
     @property
     def request_requires_value(self) -> bool:
-        return False
+        return self.multiple and not self.optional
 
 
 class GroupTagParameterModel(BaseGalaxyToolParameterModelDefinition):

diff --git a/test/functional/tools/parameters/gx_data_column_optional.xml b/test/functional/tools/parameters/gx_data_column_optional.xml
@@ -0,0 +1,28 @@
+<tool id="gx_data_column_optional" name="gx_data_column_optional" version="1.0.0">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+echo 'parameter: $parameter' >> '$output'
+    ]]></command>
+    <inputs>
+        <param name="ref_parameter" type="data" format="tabular" />
+        <param name="parameter" type="data_column" data_ref="ref_parameter" optional="true" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <param name="parameter" value="1" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 1"/>
+            </expand>
+        </test>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <expand macro="assert_output">
+                <has_line line="parameter: None"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/unit/tool_util/parameter_specification.yml b/test/unit/tool_util/parameter_specification.yml
@@ -707,6 +707,20 @@ gx_data_column:
   - { ref_parameter: {src: hda, id: abcdabcd}, parameter: 0 }
   request_invalid:
   - { ref_parameter: {src: hda, id: abcdabcd}, parameter: "0" }
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: [ 0 ] }
+  request_internal_valid:
+  - { ref_parameter: {src: hda, id: 123}, parameter: 0 }
+  request_internal_invalid:
+  - { ref_parameter: {src: hda, id: 123}, parameter: "0" }
+
+gx_data_column_optional:
+  request_valid:
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: 0 }
+  - { ref_parameter: {src: hda, id: abcdabcd} }
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: null }
+  request_invalid:
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: "0" }
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: [ 0 ] }
   request_internal_valid:
   - { ref_parameter: {src: hda, id: 123}, parameter: 0 }
   request_internal_invalid: