make optional multiple data paramaters [] in case nothing is selected

instead of [None]

Author: bernt-matthias

lib/galaxy/tool_util/xsd/galaxy.xsd

@@ -78,7 +78,7 @@ List of behavior changes associated with profile versions:
 
 ### 26.0
 
-- The ``len`` function applied on optional data parameters without a selected dataset gives ``0``. For smaller profiles ``1``
+- Optional data parameters without a selected dataset are now empty lists, i.e. ``[]``. For smaller profiles it was ``[None]``
 
 ### Examples
 

lib/galaxy/tools/evaluation.py

@@ -466,9 +466,8 @@ 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(
-                    input,
                     job_working_directory,
                     dataset_instances,
                     compute_environment=self.compute_environment,

lib/galaxy/tools/parameters/wrapped.py

@@ -118,9 +118,8 @@ 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(
-                    input,
                     None,
                     dataset_instances,
                     datatypes_registry=trans.app.datatypes_registry,

lib/galaxy/tools/wrappers.py

@@ -56,7 +56,6 @@
     from galaxy.tools import Tool
     from galaxy.tools.evaluation import ToolEvaluator
     from galaxy.tools.parameters.basic import (
-        DataToolParameter,
         SelectToolParameter,
         ToolParameter,
     )
@@ -560,7 +559,6 @@ class DatasetListWrapper(list[DatasetFilenameWrapper], ToolParameterValueWrapper
 
     def __init__(
         self,
-        input: "DataToolParameter",
         job_working_directory: Optional[str],
         datasets: Union[
             Sequence[
@@ -575,7 +573,6 @@ def __init__(
         ],
         **kwargs: Any,
     ) -> None:
-        self.input = input
         self._dataset_elements_cache: dict[str, list[DatasetFilenameWrapper]] = {}
         if not isinstance(datasets, Sequence):
             datasets = [datasets]
@@ -601,13 +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):
@@ -638,15 +637,6 @@ def __bool__(self) -> bool:
         # Fail `#if $param` checks in cheetah if optional input is not provided
         return any(self)
 
-    def __len__(self) -> int:
-        # optional data parameters are [None] if no input is given
-        # note: not self relies on the __bool__ method
-        profile = self.input.tool.profile if self.input.tool else None
-        if not self and profile is not None and Version(str(profile)) >= Version("26.0"):
-            return 0
-        else:
-            return super().__len__()
-
     __nonzero__ = __bool__
 
 
@@ -849,11 +839,6 @@ def __iter__(
             return [].__iter__()
         return self.__element_instance_list.__iter__()
 
-    # def __len__(self) -> int:
-    #     if not self.__input_supplied:
-    #         return 0
-    #     return self.__element_instance_list.__len__()
-
     def __bool__(self) -> bool:
         # Fail `#if $param` checks in cheetah is optional input
         # not specified or if resulting collection is empty.

test/functional/tools/multi_len.xml

@@ -1,12 +1,15 @@
 <tool id="multi_select" name="multi_select" 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' &&
+echo '|select_ex| = #echo len($select_ex) #' > '$output' &&
+echo '|select_ex_optional| = #echo len($select_ex_optional) #' >> '$output' &&
 
-echo 'data_ex #echo len($data_ex) #' >> '$output' &&
-echo 'data_ex_optional #echo len($data_ex_optional) #' >> '$output'
+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 $e"
+#end for
     ]]></command>
     <inputs>
         <param name="select_ex" type="select" multiple="true">
@@ -37,10 +40,10 @@ echo 'data_ex_optional #echo len($data_ex_optional) #' >> '$output'
             <param name="data_ex_optional" value="1.tabular,2.tabular"/>
             <output name="output">
                 <assert_contents>
-                    <has_line line="select_ex 3" />
-                    <has_line line="select_ex_optional 3" />
-                    <has_line line="data_ex 2" />
-                    <has_line line="data_ex_optional 2" />
+                    <has_line line="|select_ex| = 3" />
+                    <has_line line="|select_ex_optional| = 3" />
+                    <has_line line="|data_ex| = 2" />
+                    <has_line line="|data_ex_optional| = 2" />
                 </assert_contents>
             </output>
         </test>
@@ -51,10 +54,11 @@ echo 'data_ex_optional #echo len($data_ex_optional) #' >> '$output'
             <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 line="data_ex 2" />
-                    <has_line line="data_ex_optional 0" />
+                    <has_line line="|select_ex| = 3" />
+                    <has_line line="|select_ex_optional| = 0" />
+                    <has_line line="|data_ex| = 2" />
+                    <has_line line="|data_ex_optional| = 0" />
+                    <has_line_matching expression="^data_ex_optional: element" negate="true" />
                 </assert_contents>
             </output>
         </test>

test/functional/tools/multi_len_legacy.xml

@@ -1,11 +1,14 @@
 <tool id="multi_select" name="multi_select" 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' &&
+echo '|select_ex| = #echo len($select_ex) #' > '$output' &&
+echo '|select_ex_optional| = #echo len($select_ex_optional) #' >> '$output' &&
 
-echo 'data_ex #echo len($data_ex) #' >> '$output' &&
-echo 'data_ex_optional #echo len($data_ex_optional) #' >> '$output'
+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>
@@ -37,10 +40,10 @@ echo 'data_ex_optional #echo len($data_ex_optional) #' >> '$output'
             <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" />
+                    <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>
@@ -51,10 +54,11 @@ echo 'data_ex_optional #echo len($data_ex_optional) #' >> '$output'
             <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 line="data_ex 2" />
-                    <has_line line="data_ex_optional 1" /> <!-- profile behavior giving the length of [None] -->
+                    <has_line line="|select_ex| = 3" />
+                    <has_line line="|select_ex_optional| = 0" />
+                    <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"/>
                 </assert_contents>
             </output>
         </test>