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Another round of parameter model enhancements and tool tests #18678

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Aug 23, 2024
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Merged

Another round of parameter model enhancements and tool tests #18678

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c18bfa3
Tool parameter models for optional group tags.
jmchilton Aug 9, 2024
95da147
Parmaeter models for multiple=true group tags.
jmchilton Aug 9, 2024
c6ea4d3
More clarification of empty/multiple/optional select behaviors.
jmchilton Aug 9, 2024
67dc43f
Parameter models for multiple=true data column data parameters.
jmchilton Aug 9, 2024
b919f21
Parameter models for optional data columns.
jmchilton Aug 9, 2024
7011a3a
Rebuild ts schema for recent changes.
jmchilton Aug 10, 2024
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8 changes: 8 additions & 0 deletions lib/galaxy/tool_util/parameters/factory.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
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16 changes: 12 additions & 4 deletions lib/galaxy/tool_util/parameters/models.py
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Expand Up @@ -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):
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4 changes: 4 additions & 0 deletions lib/tool_shed/webapp/frontend/src/schema/schema.ts
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Expand Up @@ -745,6 +745,8 @@ export interface components {
is_dynamic?: boolean
/** Label */
label?: string | null
/** Multiple */
multiple: boolean
/** Name */
name: string
/**
Expand Down Expand Up @@ -1068,6 +1070,8 @@ export interface components {
is_dynamic?: boolean
/** Label */
label?: string | null
/** Multiple */
multiple: boolean
/** Name */
name: string
/**
Expand Down
28 changes: 28 additions & 0 deletions test/functional/tools/parameters/data_column_multiple_optional.xml
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@@ -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>
36 changes: 36 additions & 0 deletions test/functional/tools/parameters/gx_data_column_multiple.xml
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@@ -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>
28 changes: 28 additions & 0 deletions test/functional/tools/parameters/gx_data_column_optional.xml
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@@ -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>
39 changes: 39 additions & 0 deletions test/functional/tools/parameters/gx_group_tag_multiple.xml
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@@ -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>
38 changes: 38 additions & 0 deletions test/functional/tools/parameters/gx_group_tag_optional.xml
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@@ -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>
8 changes: 8 additions & 0 deletions test/functional/tools/parameters/gx_select_multiple.xml
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Expand Up @@ -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>
7 changes: 7 additions & 0 deletions test/functional/tools/parameters/gx_select_multiple_optional.xml
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Expand Up @@ -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>
60 changes: 60 additions & 0 deletions test/unit/tool_util/parameter_specification.yml
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Expand Up @@ -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' }
Expand All @@ -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
Expand Down
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