Merge pull request galaxyproject#18678 from jmchilton/parameter_models_3

Another round of parameter model enhancements and tool tests
tcollins2011 · Aug 23, 2024 · aaff1ee · aaff1ee
2 parents 2c0a703 + 7011a3a
commit aaff1ee
Show file tree

Hide file tree

Showing 11 changed files with 268 additions and 4 deletions.
diff --git a/lib/galaxy/tool_util/parameters/factory.py b/lib/galaxy/tool_util/parameters/factory.py
@@ -170,12 +170,20 @@ def _from_input_source_galaxy(input_source: InputSource) -> ToolParameterT:
                 options=static_options,
             )
         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)
+            optional = input_source.parse_optional()
             return GroupTagParameterModel(
                 name=input_source.parse_name(),
+                optional=optional,
+                multiple=multiple,
             )
         elif param_type == "baseurl":
             return BaseUrlParameterModel(

diff --git a/lib/galaxy/tool_util/parameters/models.py b/lib/galaxy/tool_util/parameters/models.py
@@ -603,32 +603,40 @@ 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 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):
     parameter_type: Literal["gx_group_tag"] = "gx_group_tag"
+    multiple: bool
 
     @property
     def py_type(self) -> Type:
-        return StrictStr
+        py_type: Type = StrictStr
+        if self.multiple:
+            py_type = list_type(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 True
+        return not self.optional
 
 
 class BaseUrlParameterModel(BaseGalaxyToolParameterModelDefinition):

diff --git a/lib/tool_shed/webapp/frontend/src/schema/schema.ts b/lib/tool_shed/webapp/frontend/src/schema/schema.ts
@@ -1243,6 +1243,8 @@ export interface components {
             is_dynamic: boolean
             /** Label */
             label?: string | null
+            /** Multiple */
+            multiple: boolean
             /** Name */
             name: string
             /**
@@ -1566,6 +1568,8 @@ export interface components {
             is_dynamic: boolean
             /** Label */
             label?: string | null
+            /** Multiple */
+            multiple: boolean
             /** Name */
             name: string
             /**

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/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/functional/tools/parameters/gx_group_tag_multiple.xml b/test/functional/tools/parameters/gx_group_tag_multiple.xml
@@ -0,0 +1,39 @@
+<tool id="gx_group_tag_multiple" name="gx_group_tag_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_collection" format="tabular" />
+        <param name="parameter" type="group_tag" data_ref="ref_parameter" multiple="true" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter">
+                <collection type="paired">
+                    <element name="forward" value="simple_line.txt" tags="group:type:single" />
+                    <element name="reverse" value="simple_line_alternative.txt" tags="group:type:split" />
+                </collection>
+            </param>
+            <param name="parameter" value="type:single,type:split" />
+            <expand macro="assert_output">
+                <has_line line="parameter: type:single,type:split"/>
+            </expand>
+        </test>
+        <test expect_failure="true">
+            <!-- interesting... this fails here but multi-selects don't -->
+            <param name="ref_parameter">
+                <collection type="paired">
+                    <element name="forward" value="simple_line.txt" tags="group:type:single" />
+                    <element name="reverse" value="simple_line_alternative.txt" tags="group:type:split" />
+                </collection>
+            </param>
+            <expand macro="assert_output">
+                <has_line line="parameter: None"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_group_tag_optional.xml b/test/functional/tools/parameters/gx_group_tag_optional.xml
@@ -0,0 +1,38 @@
+<tool id="gx_group_tag_optional" name="gx_group_tag_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_collection" format="tabular" />
+        <param name="parameter" type="group_tag" data_ref="ref_parameter" optional="true" />
+    </inputs>
+    <expand macro="simple_text_output" />
+    <tests>
+        <test>
+            <param name="ref_parameter">
+                <collection type="paired">
+                    <element name="forward" value="simple_line.txt" tags="group:type:single" />
+                    <element name="reverse" value="simple_line_alternative.txt" tags="group:type:split" />
+                </collection>
+            </param>
+            <param name="parameter" value="type:single" />
+            <expand macro="assert_output">
+                <has_line line="parameter: type:single"/>
+            </expand>
+        </test>
+        <test>
+            <param name="ref_parameter">
+                <collection type="paired">
+                    <element name="forward" value="simple_line.txt" tags="group:type:single" />
+                    <element name="reverse" value="simple_line_alternative.txt" tags="group:type:split" />
+                </collection>
+            </param>
+            <expand macro="assert_output">
+                <has_line line="parameter: None"/>
+            </expand>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/parameters/gx_select_multiple.xml b/test/functional/tools/parameters/gx_select_multiple.xml
@@ -23,5 +23,13 @@ echo '$parameter' >> '$output'
                 </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="None" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
 </tool>
diff --git a/test/functional/tools/parameters/gx_select_multiple_optional.xml b/test/functional/tools/parameters/gx_select_multiple_optional.xml
@@ -23,5 +23,12 @@ echo '$parameter' >> '$output'
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="None" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
 </tool>
diff --git a/test/unit/tool_util/parameter_specification.yml b/test/unit/tool_util/parameter_specification.yml
@@ -707,11 +707,37 @@ 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:
+  - { 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' }
@@ -726,6 +752,40 @@ gx_group_tag:
   request_internal_invalid:
   - { ref_parameter: {src: hdca, id: 123}, parameter: null }
 
+gx_group_tag_optional:
+  request_valid:
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: 'type:matched' }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: 'matched' }
+  - { ref_parameter: { src: hdca, id: abcdabcd} }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: null }
+  request_invalid:
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: 7 }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: true }
+  request_internal_valid:
+  - { ref_parameter: {src: hdca, id: 123}, parameter: 'type: matched' }
+  - { ref_parameter: {src: hdca, id: 123}, parameter: null }
+  request_internal_invalid:
+  - { ref_parameter: {src: hdca, id: 123}, parameter: 8 }
+
+
+gx_group_tag_multiple:
+  request_valid:
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: ['type:matched'] }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: ['matched'] }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: ['matched'] }
+  request_invalid:
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: 'matched' }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: 7 }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: true }
+  - { ref_parameter: { src: hdca, id: abcdabcd}, parameter: null }
+  - { ref_parameter: { src: hdca, id: abcdabcd} }
+  request_internal_valid:
+  - { ref_parameter: {src: hdca, id: 123}, parameter: ['type: matched'] }
+  request_internal_invalid:
+  - { ref_parameter: {src: hdca, id: 123}, parameter: 8 }
+  - { ref_parameter: {src: hdca, id: 123}, parameter: null }
+
+
 cwl_int:
   request_valid:
     - parameter: 5