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Allow len(x) for select and data parameters with multiple="true" #21343

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d37e29c
Allow len(x) for select and data parameters with multiple="true"
bernt-matthias Nov 21, 2025
eb0929b
remove unused function parameter
bernt-matthias Nov 21, 2025
2c0ef34
document profile version
bernt-matthias Nov 21, 2025
48cda08
make optional multiple data paramaters [] in case nothing is selected
bernt-matthias Nov 22, 2025
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4 changes: 4 additions & 0 deletions lib/galaxy/tool_util/xsd/galaxy.xsd
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,10 @@ List of behavior changes associated with profile versions:

- Do not use user preferences to store credentials for tools anymore. Use the new `<credentials>` tag in the `<requirements>` section of the tool XML instead.

### 26.0

- Optional data parameters without a selected dataset are now empty lists, i.e. ``[]``. For smaller profiles it was ``[None]``

### Examples

A normal tool:
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6 changes: 2 additions & 4 deletions lib/galaxy/tools/evaluation.py
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Expand Up @@ -466,7 +466,7 @@ def __populate_wrappers(self, param_dict, input_datasets, job_working_directory)
def wrap_input(input_values, input):
value = input_values[input.name]
if isinstance(input, DataToolParameter) and input.multiple:
dataset_instances = DatasetListWrapper.to_dataset_instances(value)
dataset_instances = DatasetListWrapper.to_dataset_instances(value, self.tool.profile)
input_values[input.name] = DatasetListWrapper(
job_working_directory,
dataset_instances,
Expand Down Expand Up @@ -510,9 +510,7 @@ def wrap_input(input_values, input):
input, value, other_values=param_dict, compute_environment=self.compute_environment
)
else:
input_values[input.name] = InputValueWrapper(
input, value, param_dict, profile=self.tool and self.tool.profile or None
)
input_values[input.name] = InputValueWrapper(input, value, param_dict)

# HACK: only wrap if check_values is not false, this deals with external
# tools where the inputs don't even get passed through. These
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4 changes: 2 additions & 2 deletions lib/galaxy/tools/parameters/wrapped.py
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Expand Up @@ -118,7 +118,7 @@ def wrap_values(self, inputs: "ToolInputsT", input_values: dict, skip_missing_va
values = value
self.wrap_values(input.inputs, values, skip_missing_values=skip_missing_values)
elif isinstance(input, DataToolParameter) and input.multiple:
dataset_instances = DatasetListWrapper.to_dataset_instances(value)
dataset_instances = DatasetListWrapper.to_dataset_instances(value, self.tool.profile)
input_values[input.name] = DatasetListWrapper(
None,
dataset_instances,
Expand Down Expand Up @@ -148,7 +148,7 @@ def wrap_values(self, inputs: "ToolInputsT", input_values: dict, skip_missing_va
)
else:
assert isinstance(input, ToolParameter)
input_values[input.name] = InputValueWrapper(input, value, incoming, tool.profile)
input_values[input.name] = InputValueWrapper(input, value, incoming)


def make_dict_copy(from_dict: dict):
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11 changes: 9 additions & 2 deletions lib/galaxy/tools/wrappers.py
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Expand Up @@ -18,6 +18,7 @@
Union,
)

from packaging.version import Version
from typing_extensions import (
Self,
TypeAlias,
Expand Down Expand Up @@ -129,7 +130,6 @@ def __init__(
input: "ToolParameter",
value: Optional[str],
other_values: Optional[dict[str, str]] = None,
profile: Optional[float] = None,
) -> None:
self.input = input
if value is None and input.type == "text":
Expand Down Expand Up @@ -284,6 +284,11 @@ def __iter__(self) -> Iterable[str]:
raise Exception("Tried to iterate over a non-multiple parameter.")
return self.value.__iter__()

def __len__(self) -> int:
if not self.input.multiple:
raise Exception("Non-multiple parameter has no len().")
return self.value.__len__()


class DatasetFilenameWrapper(ToolParameterValueWrapper):
"""
Expand Down Expand Up @@ -593,13 +598,15 @@ def to_wrapper(
@staticmethod
def to_dataset_instances(
dataset_instance_sources: Any,
profile: Optional[float],
) -> list[Union[None, DatasetInstance]]:
dataset_instances: list[Optional[DatasetInstance]] = []
if not isinstance(dataset_instance_sources, list):
dataset_instance_sources = [dataset_instance_sources]
for dataset_instance_source in dataset_instance_sources:
if dataset_instance_source is None:
dataset_instances.append(dataset_instance_source)
if profile is None or Version(str(profile)) < Version("26.0"):
dataset_instances.append(dataset_instance_source)
elif getattr(dataset_instance_source, "history_content_type", None) == "dataset":
dataset_instances.append(dataset_instance_source)
elif getattr(dataset_instance_source, "hda", None):
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73 changes: 73 additions & 0 deletions test/functional/tools/multi_len.xml
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@@ -0,0 +1,73 @@
<tool id="multi_len" name="multi_len" version="1.0.0" profile="26.0">
<description>test len() parameters allowing multiple</description>
<command><![CDATA[
echo '|select_ex| = #echo len($select_ex) #' > '$output' &&
echo '|select_ex_optional| = #echo len($select_ex_optional) #' >> '$output' &&
#for i, e in enumerate($select_ex_optional)
&& echo "select_ex_optional: element $i is $e"
#end for

echo '|data_ex| = #echo len($data_ex) #' >> '$output' &&
echo '|data_ex_optional| = #echo len($data_ex_optional) #' >> '$output'

#for i, e in enumerate($data_ex_optional)
&& echo "data_ex_optional: element $i is $e"
#end for
]]></command>
<inputs>
<param name="select_ex" type="select" multiple="true">
<option value="1">1</option>
<option value="2">2</option>
<option value="3">3</option>
<option value="4">4</option>
<option value="5">5</option>
</param>
<param name="select_ex_optional" type="select" multiple="true" optional="true">
<option value="1">1</option>
<option value="2">2</option>
<option value="3">3</option>
<option value="4">4</option>
<option value="5">5</option>
</param>
<param name="data_ex" type="data" format="data" multiple="true"/>
<param name="data_ex_optional" type="data" format="data" multiple="true" optional="true"/>
</inputs>
<outputs>
<data name="output" format="txt" />
</outputs>
<tests>
<test>
<param name="select_ex" value="1,2,3" />
<param name="select_ex_optional" value="1,2,3" />
<param name="data_ex" value="1.tabular,2.tabular"/>
<param name="data_ex_optional" value="1.tabular,2.tabular"/>
<output name="output">
<assert_contents>
<has_line line="|select_ex| = 3" />
<has_line line="|select_ex_optional| = 3" />
<has_line line="|data_ex| = 2" />
<has_line line="|data_ex_optional| = 2" />
</assert_contents>
</output>
</test>
<test>
<param name="select_ex" value="1,2,3" />
<param name="select_ex_optional" value_json="null" />
<param name="data_ex" value="1.tabular,2.tabular"/>
<param name="data_ex_optional" value_json="null"/>
<output name="output">
<assert_contents>
<has_line line="|select_ex| = 3" />
<has_line line="|select_ex_optional| = 0" />
<has_line_matching expression="^select_ex_optional: element" negate="true" />
<has_line line="|data_ex| = 2" />
<has_line line="|data_ex_optional| = 0" />
<has_line_matching expression="^data_ex_optional: element" negate="true" />
<has_n_lines n="4"/>
</assert_contents>
</output>
</test>
</tests>
<help>
</help>
</tool>
73 changes: 73 additions & 0 deletions test/functional/tools/multi_len_legacy.xml
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@@ -0,0 +1,73 @@
<tool id="multi_len_legacy" name="multi_len_legacy" version="1.0.0" profile="25.1">
<description>test len() parameters allowing multiple for 25.1</description>
<command><![CDATA[
echo '|select_ex| = #echo len($select_ex) #' > '$output' &&
echo '|select_ex_optional| = #echo len($select_ex_optional) #' >> '$output' &&
#for i, e in enumerate($select_ex_optional)
&& echo "select_ex_optional: element $i is $e"
#end for

echo '|data_ex| = #echo len($data_ex) #' >> '$output' &&
echo '|data_ex_optional| = #echo len($data_ex_optional) #' >> '$output'
#for i, e in enumerate($data_ex_optional)
&& echo "data_ex_optional: element $i is $e"
#end for

]]></command>
<inputs>
<param name="select_ex" type="select" multiple="true">
<option value="1">1</option>
<option value="2">2</option>
<option value="3">3</option>
<option value="4">4</option>
<option value="5">5</option>
</param>
<param name="select_ex_optional" type="select" multiple="true" optional="true">
<option value="1">1</option>
<option value="2">2</option>
<option value="3">3</option>
<option value="4">4</option>
<option value="5">5</option>
</param>
<param name="data_ex" type="data" format="data" multiple="true"/>
<param name="data_ex_optional" type="data" format="data" multiple="true" optional="true"/>
</inputs>
<outputs>
<data name="output" format="txt" />
</outputs>
<tests>
<test>
<param name="select_ex" value="1,2,3" />
<param name="select_ex_optional" value="1,2,3" />
<param name="data_ex" value="1.tabular,2.tabular"/>
<param name="data_ex_optional" value="1.tabular,2.tabular"/>
<output name="output">
<assert_contents>
<has_line line="|select_ex| = 3" />
<has_line line="|select_ex_optional| = 3" />
<has_line line="|data_ex| = 2" />
<has_line line="|data_ex_optional| = 2" />
</assert_contents>
</output>
</test>
<test>
<param name="select_ex" value="1,2,3" />
<param name="select_ex_optional" value_json="null" />
<param name="data_ex" value="1.tabular,2.tabular"/>
<param name="data_ex_optional" value_json="null"/>
<output name="output">
<assert_contents>
<has_line line="|select_ex| = 3" />
<has_line line="|select_ex_optional| = 0" />
<has_line_matching expression="^select_ex_optional: element" negate="true" />
<has_line line="|data_ex| = 2" />
<has_line line="|data_ex_optional| = 1" /> <!-- profile behavior giving the length of [None] -->
<has_line line="data_ex_optional: element 0 is None"/>
<has_n_lines n="5"/>
</assert_contents>
</output>
</test>
</tests>
<help>
</help>
</tool>
2 changes: 2 additions & 0 deletions test/functional/tools/sample_tool_conf.xml
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Expand Up @@ -27,6 +27,8 @@
<tool file="help_features_rst.xml" />
<tool file="help_features_markdown.xml" />
<tool file="select_from_url.xml" />
<tool file="multi_len.xml" />
<tool file="multi_len_legacy.xml" />
<tool file="multi_select.xml" />
<tool file="multi_output.xml" />
<tool file="multi_output_configured.xml" />
Expand Down
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