De-couple XML from tool interface for test collections.

Keep more in JSON longer so we can apply less custom model objects for validation and stuff. The interface is returning more pure json now.

lib/galaxy/tool_util/parser/interface.py

@@ -19,6 +19,7 @@
 import packaging.version
 from pydantic import BaseModel
 from typing_extensions import (
+    Literal,
     NotRequired,
     TypedDict,
 )
@@ -549,6 +550,19 @@ def parse_input_sources(self) -> List[InputSource]:
         """Return a list of InputSource objects."""
 
 
+class TestCollectionDefElementDict(TypedDict):
+    element_identifier: str
+    element_definition: Union["TestCollectionDefDict", "ToolSourceTestInput"]
+
+
+class TestCollectionDefDict(TypedDict):
+    model_class: Literal["TestCollectionDef"]
+    attributes: Dict[str, Any]
+    collection_type: str
+    elements: List[TestCollectionDefElementDict]
+    name: str
+
+
 class TestCollectionDef:
     __test__ = False  # Prevent pytest from discovering this class (issue #12071)
 
@@ -558,30 +572,7 @@ def __init__(self, attrib, name, collection_type, elements):
         self.elements = elements
         self.name = name
 
-    @staticmethod
-    def from_xml(elem, parse_param_elem):
-        elements = []
-        attrib = dict(elem.attrib)
-        collection_type = attrib["type"]
-        name = attrib.get("name", "Unnamed Collection")
-        for element in elem.findall("element"):
-            element_attrib = dict(element.attrib)
-            element_identifier = element_attrib["name"]
-            nested_collection_elem = element.find("collection")
-            if nested_collection_elem is not None:
-                element_definition = TestCollectionDef.from_xml(nested_collection_elem, parse_param_elem)
-            else:
-                element_definition = parse_param_elem(element)
-            elements.append({"element_identifier": element_identifier, "element_definition": element_definition})
-
-        return TestCollectionDef(
-            attrib=attrib,
-            collection_type=collection_type,
-            elements=elements,
-            name=name,
-        )
-
-    def to_dict(self):
+    def to_dict(self) -> TestCollectionDefDict:
         def element_to_dict(element_dict):
             element_identifier, element_def = element_dict["element_identifier"], element_dict["element_definition"]
             if isinstance(element_def, TestCollectionDef):
@@ -600,7 +591,7 @@ def element_to_dict(element_dict):
         }
 
     @staticmethod
-    def from_dict(as_dict):
+    def from_dict(as_dict: TestCollectionDefDict):
         assert as_dict["model_class"] == "TestCollectionDef"
 
         def element_from_dict(element_dict):

lib/galaxy/tool_util/parser/xml.py

@@ -45,8 +45,9 @@
     PageSource,
     PagesSource,
     RequiredFiles,
-    TestCollectionDef,
     TestCollectionOutputDef,
+    TestCollectionDefDict,
+    TestCollectionDefElementDict,
     ToolSource,
     ToolSourceTest,
     ToolSourceTestInput,
@@ -790,7 +791,7 @@ def __parse_output_collection_elem(output_collection_elem, profile=None):
 def __parse_element_tests(parent_element, profile=None):
     element_tests = {}
     for idx, element in enumerate(parent_element.findall("element")):
-        element_attrib = dict(element.attrib)
+        element_attrib: dict = dict(element.attrib)
         identifier = element_attrib.pop("name", None)
         if identifier is None:
             raise Exception("Test primary dataset does not have a 'identifier'")
@@ -999,6 +1000,30 @@ def __parse_inputs_elems(test_elem, i) -> ToolSourceTestInputs:
     return raw_inputs
 
 
+def _test_collection_def_dict(elem: Element) -> TestCollectionDefDict:
+    elements: TestCollectionDefElementDict = []
+    attrib: dict = dict(elem.attrib)
+    collection_type = attrib["type"]
+    name = attrib.get("name", "Unnamed Collection")
+    for element in elem.findall("element"):
+        element_attrib = dict(element.attrib)
+        element_identifier = element_attrib["name"]
+        nested_collection_elem = element.find("collection")
+        if nested_collection_elem is not None:
+            element_definition = _test_collection_def_dict(nested_collection_elem)
+        else:
+            element_definition = __parse_param_elem(element)
+        elements.append({"element_identifier": element_identifier, "element_definition": element_definition})
+
+    return TestCollectionDefDict(
+        model_class="TestCollectionDef",
+        attributes=attrib,
+        collection_type=collection_type,
+        elements=elements,
+        name=name,
+    )
+
+
 def __parse_param_elem(param_elem, i=0) -> ToolSourceTestInput:
     attrib: ToolSourceTestInputAttributes = dict(param_elem.attrib)
     if "values" in attrib:
@@ -1037,7 +1062,7 @@ def __parse_param_elem(param_elem, i=0) -> ToolSourceTestInput:
             elif child.tag == "edit_attributes":
                 attrib["edit_attributes"].append(child)
             elif child.tag == "collection":
-                attrib["collection"] = TestCollectionDef.from_xml(child, __parse_param_elem)
+                attrib["collection"] = _test_collection_def_dict(child)
         if composite_data_name:
             # Composite datasets need implicit renaming;
             # inserted at front of list so explicit declarations

lib/galaxy/tool_util/verify/interactor.py

@@ -38,6 +38,7 @@
 from galaxy.tool_util.parser.interface import (
     AssertionList,
     TestCollectionDef,
+    TestCollectionDefDict,
     TestCollectionOutputDef,
     TestSourceTestOutputColllection,
     ToolSourceTestOutputs,
@@ -1749,7 +1750,8 @@ def expanded_inputs_from_json(expanded_inputs_json: ExpandedToolInputsJsonified)
     loaded_inputs: ExpandedToolInputs = {}
     for key, value in expanded_inputs_json.items():
         if isinstance(value, dict) and value.get("model_class"):
-            loaded_inputs[key] = TestCollectionDef.from_dict(value)
+            collection_def_dict = cast(TestCollectionDefDict, value)
+            loaded_inputs[key] = TestCollectionDef.from_dict(collection_def_dict)
         else:
             loaded_inputs[key] = value
     return loaded_inputs

lib/galaxy/tool_util/verify/parse.py

@@ -10,6 +10,7 @@
 
 from galaxy.tool_util.parser.interface import (
     InputSource,
+    TestCollectionDef,
     ToolSource,
     ToolSourceTest,
     ToolSourceTestInputs,
@@ -246,7 +247,8 @@ def _process_raw_inputs(
                     processed_value = param_value
                 elif param_type == "data_collection":
                     assert "collection" in param_extra
-                    collection_def = param_extra["collection"]
+                    collection_dict = param_extra["collection"]
+                    collection_def = TestCollectionDef.from_dict(collection_dict)
                     for input_dict in collection_def.collect_inputs():
                         name = input_dict["name"]
                         value = input_dict["value"]