Parameter models for multiple=true data column data parameters.

galaxyproject · Aug 11, 2024 · 67dc43f · 67dc43f
1 parent c6ea4d3
commit 67dc43f
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Showing 5 changed files with 83 additions and 1 deletion.
diff --git a/lib/galaxy/tool_util/parameters/factory.py b/lib/galaxy/tool_util/parameters/factory.py
@@ -170,8 +170,10 @@ def _from_input_source_galaxy(input_source: InputSource) -> ToolParameterT:
                 options=static_options,
             )
         elif param_type == "data_column":
+            multiple = input_source.get_bool("multiple", False)
             return DataColumnParameterModel(
                 name=input_source.parse_name(),
+                multiple=multiple,
             )
         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
@@ -603,10 +603,14 @@ def any_drill_down_options_selected(options: List[DrillDownOptionsDict]) -> bool
 
 class DataColumnParameterModel(BaseGalaxyToolParameterModelDefinition):
     parameter_type: Literal["gx_data_column"] = "gx_data_column"
+    multiple: bool
 
     @property
     def py_type(self) -> Type:
-        return StrictInt
+        py_type: Type = StrictInt
+        if self.multiple:
+            py_type = list_type(py_type)
+        return py_type
 
     def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
         return dynamic_model_information_from_py_type(self, self.py_type)

diff --git a/test/functional/tools/parameters/data_column_multiple_optional.xml b/test/functional/tools/parameters/data_column_multiple_optional.xml
@@ -0,0 +1,28 @@
+<tool id="gx_data_column_multiple_optional" name="gx_data_column_multiple_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" multiple="true" optional="true" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter" value="2.tabular" />
+            <param name="parameter" value="1,2,3" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 1,2,3"/>
+            </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/functional/tools/parameters/gx_data_column_multiple.xml b/test/functional/tools/parameters/gx_data_column_multiple.xml
@@ -0,0 +1,36 @@
+<tool id="gx_data_column_multiple" name="gx_data_column_multiple" 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" multiple="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" />
+            <param name="parameter" value="1,2,3" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 1,2,3"/>
+            </expand>
+        </test>
+        <!-- these parameters are not implicitly optional! -->
+        <test expect_failure="true">
+            <param name="ref_parameter" value="2.tabular" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 1"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/unit/tool_util/parameter_specification.yml b/test/unit/tool_util/parameter_specification.yml
@@ -712,6 +712,18 @@ gx_data_column:
   request_internal_invalid:
   - { ref_parameter: {src: hda, id: 123}, parameter: "0" }
 
+gx_data_column_multiple:
+  request_valid:
+  - { 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" }
+  - { ref_parameter: {src: hda, id: 123}, parameter: 0 }
+
 gx_group_tag:
   request_valid:
   - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: 'type:matched' }