[26.0] Fix IndexError in SplitPairedAndUnpairedTool for unpaired elements

lib/galaxy/managers/collections.py

@@ -354,6 +354,7 @@ def create_dataset_collection(
         # else if elements is set, it better be an ordered dict!
 
         if elements is not self.ELEMENTS_UNINITIALIZED:
+            self._validate_nested_collection_elements(collection_type_description, elements)
             type_plugin = collection_type_description.rank_type_plugin()
             dataset_collection = builder.build_collection(
                 type_plugin, elements, fields=fields, column_definitions=column_definitions, rows=rows
@@ -577,6 +578,32 @@ def __persist(
             session.commit()
         return dataset_collection_instance
 
+    def _validate_nested_collection_elements(self, collection_type_description, elements) -> None:
+        """For nested collection types (e.g. ``list:paired_or_unpaired``), verify that
+        every element value is a :class:`DatasetCollection` whose ``collection_type``
+        matches the expected sub-collection type. Otherwise creating a
+        ``list:paired_or_unpaired`` from raw HDAs would silently produce a
+        structurally invalid collection that downstream tools cannot handle.
+        """
+        if not collection_type_description.has_subcollections():
+            return
+        if not isinstance(elements, dict):
+            return
+        expected_sub = collection_type_description.subcollection_type_description().collection_type
+        for identifier, value in elements.items():
+            if isinstance(value, DatasetCollection) and value.collection_type == expected_sub:
+                continue
+            if isinstance(value, DatasetCollection):
+                actual = f"a collection of type '{value.collection_type}'"
+            elif getattr(value, "history_content_type", None) == "dataset":
+                actual = "a dataset"
+            else:
+                actual = type(value).__name__
+            raise RequestParameterInvalidException(
+                f"Element '{identifier}' of collection type '{collection_type_description.collection_type}' "
+                f"must be a sub-collection of type '{expected_sub}', got {actual}."
+            )
+
     def __recursively_create_collections_for_identifiers(
         self, trans, element_identifiers, hide_source_items: bool, copy_elements: bool, history=None
     ):

lib/galaxy/tools/__init__.py

@@ -62,6 +62,7 @@
     ToolRequest,
 )
 from galaxy.model.dataset_collections.matching import MatchingCollections
+from galaxy.model.dataset_collections.types.paired_or_unpaired import SINGLETON_IDENTIFIER
 from galaxy.model.dataset_collections.types.sample_sheet_workbook import _sample_sheet_to_list_collection_type
 from galaxy.objectstore import ObjectStorePopulator
 from galaxy.schema.credentials import CredentialsContext
@@ -4036,14 +4037,26 @@ def produce_outputs(self, trans, out_data, output_collections, incoming, history
 
         def _handle_unpaired(dce):
             element_identifier = dce.element_identifier
-            assert getattr(dce.element_object, "history_content_type", None) == "dataset"
-            copied_value = dce.element_object.copy(copy_tags=dce.element_object.tags, flush=False)
+            element_object = dce.element_object
+            # In list:paired_or_unpaired collections, unpaired elements are
+            # wrapped in a 1-element sub-collection. Unwrap to get the dataset.
+            if getattr(element_object, "elements", None):
+                inner_element = element_object.elements[0]
+                assert inner_element.element_identifier == SINGLETON_IDENTIFIER
+                element_object = inner_element.element_object
+            assert element_object.history_content_type == "dataset"
+            copied_value = element_object.copy(copy_tags=element_object.tags, flush=False)
             unpaired_dce_copies[element_identifier] = copied_value
             unpaired_dce_columns[element_identifier] = dce.columns
 
         def _handle_paired(dce):
             element_identifier = dce.element_identifier
             copied_value = dce.element_object.copy(flush=False)
+            # Normalize to 'paired' for list:paired output, since a
+            # list:paired_or_unpaired input may contain 2-element
+            # paired_or_unpaired sub-collections that are structurally
+            # equivalent to paired but carry the wider collection_type.
+            copied_value.collection_type = "paired"
             paired_dce_copies[element_identifier] = copied_value
             paired_datasets.append(copied_value.elements[0].element_object)
             paired_datasets.append(copied_value.elements[1].element_object)
@@ -4057,7 +4070,8 @@ def _handle_paired(dce):
                 _handle_paired(element)
         elif collection_type == "list:paired_or_unpaired":
             for element in collection.elements:
-                if getattr(element.element_object, "history_content_type", None) == "dataset":
+                sub_collection = element.element_object
+                if len(sub_collection.elements) == 1:
                     _handle_unpaired(element)
                 else:
                     _handle_paired(element)

lib/galaxy/tools/split_paired_and_unpaired.xml

@@ -76,14 +76,20 @@
       <param name="input">
         <collection type="list:paired_or_unpaired">
           <element name="el1">
-            <collection type="paired">
+            <collection type="paired_or_unpaired">
               <element name="forward" value="simple_line.txt" />
               <element name="reverse" value="simple_line_alternative.txt" />
             </collection>
           </element>
-          <element name="el2" value="simple_line.txt">
+          <element name="el2">
+            <collection type="paired_or_unpaired">
+              <element name="unpaired" value="simple_line.txt" />
+            </collection>
           </element>
-          <element name="el3" value="simple_line_alternative.txt">
+          <element name="el3">
+            <collection type="paired_or_unpaired">
+              <element name="unpaired" value="simple_line_alternative.txt" />
+            </collection>
           </element>
         </collection>
       </param>

lib/galaxy_test/api/test_dataset_collections.py

@@ -7,6 +7,7 @@
 from galaxy.tool_util_models.sample_sheet import SampleSheetColumnDefinitions
 from galaxy.util import galaxy_root_path
 from galaxy_test.base.api_asserts import (
+    assert_error_message_contains,
     assert_has_key,
     assert_object_id_error,
     assert_status_code_is,
@@ -152,6 +153,30 @@ def test_create_paried_or_unpaired(self, history_id):
         returned_collections = dataset_collection["elements"]
         assert len(returned_collections) == 1, dataset_collection
 
+    def test_create_list_paired_or_unpaired_rejects_raw_hda_child(self, history_id):
+        element_identifiers = self.dataset_collection_populator.list_identifiers(history_id, contents=[("el1", "hi")])
+        payload = dict(
+            instance_type="history",
+            history_id=history_id,
+            element_identifiers=element_identifiers,
+            collection_type="list:paired_or_unpaired",
+        )
+        create_response = self._post("dataset_collections", payload, json=True)
+        assert_status_code_is(create_response, 400)
+        assert_error_message_contains(create_response, "sub-collection of type 'paired_or_unpaired'")
+
+    def test_create_list_paired_rejects_raw_hda_child(self, history_id):
+        element_identifiers = self.dataset_collection_populator.list_identifiers(history_id, contents=[("el1", "hi")])
+        payload = dict(
+            instance_type="history",
+            history_id=history_id,
+            element_identifiers=element_identifiers,
+            collection_type="list:paired",
+        )
+        create_response = self._post("dataset_collections", payload, json=True)
+        assert_status_code_is(create_response, 400)
+        assert_error_message_contains(create_response, "sub-collection of type 'paired'")
+
     def test_create_record(self, history_id):
         contents = [
             ("condition", "1\t2\t3"),

lib/galaxy_test/workflow/split_paired_and_unpaired.gxwf-tests.yml

@@ -0,0 +1,48 @@
+- doc: |
+    Test splitting a list:paired_or_unpaired collection with mixed paired
+    and unpaired elements into separate paired and unpaired output collections.
+  job:
+    input_collection:
+      class: Collection
+      collection_type: list:paired_or_unpaired
+      elements:
+        - identifier: el1
+          class: Collection
+          type: paired_or_unpaired
+          elements:
+            - identifier: forward
+              class: File
+              contents: "forward content"
+            - identifier: reverse
+              class: File
+              contents: "reverse content"
+        - identifier: el2
+          class: Collection
+          type: paired_or_unpaired
+          elements:
+            - identifier: unpaired
+              class: File
+              contents: "unpaired content"
+  outputs:
+    output_unpaired:
+      class: Collection
+      collection_type: list
+      elements:
+        el2:
+          asserts:
+            - that: has_text
+              text: "unpaired content"
+    output_paired:
+      class: Collection
+      collection_type: list:paired
+      elements:
+        el1:
+          elements:
+            forward:
+              asserts:
+                - that: has_text
+                  text: "forward content"
+            reverse:
+              asserts:
+                - that: has_text
+                  text: "reverse content"

lib/galaxy_test/workflow/split_paired_and_unpaired.gxwf.yml

@@ -0,0 +1,15 @@
+class: GalaxyWorkflow
+inputs:
+  input_collection:
+    type: collection
+    collection_type: list:paired_or_unpaired
+outputs:
+  output_unpaired:
+    outputSource: split/output_unpaired
+  output_paired:
+    outputSource: split/output_paired
+steps:
+  split:
+    tool_id: '__SPLIT_PAIRED_AND_UNPAIRED__'
+    in:
+      input: input_collection