Work toward data column support in tool parameter meta models.

galaxyproject · Aug 5, 2024 · 2f19d2c · 2f19d2c
1 parent cb3ec1f
commit 2f19d2c
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Showing 4 changed files with 67 additions and 0 deletions.
diff --git a/lib/galaxy/tool_util/parameters/factory.py b/lib/galaxy/tool_util/parameters/factory.py
@@ -29,6 +29,7 @@
     CwlStringParameterModel,
     CwlUnionParameterModel,
     DataCollectionParameterModel,
+    DataColumnParameterModel,
     DataParameterModel,
     DrillDownParameterModel,
     FloatParameterModel,
@@ -159,6 +160,10 @@ def _from_input_source_galaxy(input_source: InputSource) -> ToolParameterT:
                 hierarchy=hierarchy,
                 options=static_options,
             )
+        elif param_type == "data_column":
+            return DataColumnParameterModel(
+                name=input_source.parse_name(),
+            )
         else:
             raise Exception(f"Unknown Galaxy parameter type {param_type}")
     elif input_type == "conditional":

diff --git a/lib/galaxy/tool_util/parameters/models.py b/lib/galaxy/tool_util/parameters/models.py
@@ -554,6 +554,21 @@ def request_requires_value(self) -> bool:
         return self.multiple and not self.optional
 
 
+class DataColumnParameterModel(BaseGalaxyToolParameterModelDefinition):
+    parameter_type: Literal["gx_data_column"] = "gx_data_column"
+
+    @property
+    def py_type(self) -> Type:
+        return StrictInt
+
+    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
+
+
 DiscriminatorType = Union[bool, str]
 
 
@@ -883,6 +898,7 @@ def request_requires_value(self) -> bool:
     SelectParameterModel,
     DataParameterModel,
     DataCollectionParameterModel,
+    DataColumnParameterModel,
     DirectoryUriParameterModel,
     RulesParameterModel,
     DrillDownParameterModel,

diff --git a/test/functional/tools/parameters/gx_data_column.xml b/test/functional/tools/parameters/gx_data_column.xml
@@ -0,0 +1,36 @@
+<tool id="gx_data_column" name="gx_data_column" 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="2" />
+            <expand macro="assert_output">
+                <has_line line="parameter: 2"/>
+            </expand>
+        </test>
+        <!-- these parameters are implicitly optional -->
+        <test>
+            <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
@@ -631,6 +631,16 @@ gx_drill_down_exact:
   - parameter: c
   - parameter: {}
 
+gx_data_column:
+  request_valid:
+  - { ref_parameter: {src: hda, id: abcdabcd}, parameter: 0 }
+  request_invalid:
+  - { 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" }
+
 cwl_int:
   request_valid:
     - parameter: 5