Rework test case validation schema.

lib/galaxy/tool_util/parameters/__init__.py

@@ -62,6 +62,7 @@
     repeat_inputs_to_array,
     validate_explicit_conditional_test_value,
     visit_input_values,
+    VISITOR_NO_REPLACEMENT,
 )
 
 __all__ = (
@@ -116,6 +117,7 @@
     "keys_starting_with",
     "visit_input_values",
     "repeat_inputs_to_array",
+    "VISITOR_NO_REPLACEMENT",
     "decode",
     "encode",
     "WorkflowStepToolState",

lib/galaxy/tool_util/parameters/case.py

@@ -12,10 +12,12 @@
 from packaging.version import Version
 
 from galaxy.tool_util.parser.interface import (
+    TestCollectionDef,
     ToolSource,
     ToolSourceTest,
     ToolSourceTestInput,
     ToolSourceTestInputs,
+    xml_data_input_to_json,
 )
 from galaxy.util import asbool
 from .factory import input_models_for_tool_source
@@ -25,6 +27,7 @@
     ConditionalWhen,
     DataCollectionParameterModel,
     DataColumnParameterModel,
+    DataParameterModel,
     FloatParameterModel,
     IntegerParameterModel,
     RepeatParameterModel,
@@ -250,7 +253,22 @@ def _merge_into_state(
         test_input = _input_for(state_path, inputs)
         if test_input is not None:
             if isinstance(tool_input, (DataCollectionParameterModel,)):
-                input_value = test_input.get("attributes", {}).get("collection")
+                input_value = TestCollectionDef.from_dict(
+                    test_input.get("attributes", {}).get("collection")
+                ).test_format_to_dict()
+            elif isinstance(tool_input, (DataParameterModel,)):
+                data_tool_input = cast(DataParameterModel, tool_input)
+                if data_tool_input.multiple:
+                    test_input_values = test_input["value"].split(",")
+                    input_value_list = []
+                    for test_input_value in test_input_values:
+                        instance_test_input = test_input.copy()
+                        instance_test_input["value"] = test_input_value
+                        input_value = xml_data_input_to_json(test_input)
+                        input_value_list.append(input_value)
+                    input_value = input_value_list
+                else:
+                    input_value = xml_data_input_to_json(test_input)
             else:
                 input_value = test_input["value"]
                 input_value = legacy_from_string(tool_input, input_value, warnings, profile)

lib/galaxy/tool_util/parameters/models.py

@@ -41,7 +41,8 @@
 from galaxy.exceptions import RequestParameterInvalidException
 from galaxy.tool_util.parser.interface import (
     DrillDownOptionsDict,
-    TestCollectionDefDict,
+    JsonTestCollectionDefDict,
+    JsonTestDatasetDefDict,
 )
 from ._types import (
     cast_as_type,
@@ -312,9 +313,9 @@ def py_type_internal(self) -> Type:
     def py_type_test_case(self) -> Type:
         base_model: Type
         if self.multiple:
-            base_model = str
+            base_model = list_type(JsonTestDatasetDefDict)
         else:
-            base_model = str
+            base_model = JsonTestDatasetDefDict
         return optional_if_needed(base_model, self.optional)
 
     def pydantic_template(self, state_representation: StateRepresentationT) -> DynamicModelInformation:
@@ -372,7 +373,7 @@ def pydantic_template(self, state_representation: StateRepresentationT) -> Dynam
         elif state_representation == "workflow_step_linked":
             return dynamic_model_information_from_py_type(self, ConnectedValue)
         elif state_representation == "test_case_xml":
-            return dynamic_model_information_from_py_type(self, TestCollectionDefDict)
+            return dynamic_model_information_from_py_type(self, JsonTestCollectionDefDict)
         else:
             raise NotImplementedError(
                 f"Have not implemented data collection parameter models for state representation {state_representation}"
@@ -1179,9 +1180,7 @@ def to_simple_model(input_parameter: Union[ToolParameterModel, ToolParameterT])
         return cast(ToolParameterT, input_parameter)
 
 
-def simple_input_models(
-    parameters: Union[List[ToolParameterModel], List[ToolParameterT]]
-) -> Iterable[ToolParameterT]:
+def simple_input_models(parameters: Union[List[ToolParameterModel], List[ToolParameterT]]) -> Iterable[ToolParameterT]:
     return [to_simple_model(m) for m in parameters]
 
 

lib/galaxy/tool_util/parser/interface.py

@@ -8,6 +8,7 @@
 from os.path import join
 from typing import (
     Any,
+    cast,
     Dict,
     List,
     Optional,
@@ -550,7 +551,8 @@ def parse_input_sources(self) -> List[InputSource]:
         """Return a list of InputSource objects."""
 
 
-TestCollectionDefElementObject = Union["TestCollectionDefDict", "ToolSourceTestInput"]
+AnyTestCollectionDefDict = Union["JsonTestCollectionDefDict", "XmlTestCollectionDefDict"]
+TestCollectionDefElementObject = Union[AnyTestCollectionDefDict, "ToolSourceTestInput"]
 TestCollectionAttributeDict = Dict[str, Any]
 CollectionType = str
 
@@ -560,14 +562,96 @@ class TestCollectionDefElementDict(TypedDict):
     element_definition: TestCollectionDefElementObject
 
 
-class TestCollectionDefDict(TypedDict):
+# two versions of collection inputs can be parsed out, XmlTestCollectionDefDict is historically
+# used by tools and Galaxy internals and exposed in the API via the test definition endpoints for
+# tool execution. JsonTestCollectionDefDict is the format consumed by Planemo that mirrors a CWL
+# way of defining inputs.
+class XmlTestCollectionDefDict(TypedDict):
     model_class: Literal["TestCollectionDef"]
     attributes: TestCollectionAttributeDict
     collection_type: CollectionType
     elements: List[TestCollectionDefElementDict]
     name: str
 
 
+JsonTestDatasetDefDict = TypedDict(
+    "JsonTestDatasetDefDict",
+    {
+        "class": Literal["File"],
+        "path": NotRequired[Optional[str]],
+        "location": NotRequired[Optional[str]],
+        "name": NotRequired[Optional[str]],
+        "dbkey": NotRequired[Optional[str]],
+        "filetype": NotRequired[Optional[str]],
+        "composite_data": NotRequired[Optional[List[str]]],
+        "tags": NotRequired[Optional[List[str]]],
+    },
+)
+
+JsonTestCollectionDefElementDict = Union[
+    "JsonTestCollectionDefDatasetElementDict", "JsonTestCollectionDefCollectionElementDict"
+]
+JsonTestCollectionDefDatasetElementDict = TypedDict(
+    "JsonTestCollectionDefDatasetElementDict",
+    {
+        "identifier": str,
+        "class": Literal["File"],
+        "path": NotRequired[Optional[str]],
+        "location": NotRequired[Optional[str]],
+        "name": NotRequired[Optional[str]],
+        "dbkey": NotRequired[Optional[str]],
+        "filetype": NotRequired[Optional[str]],
+        "composite_data": NotRequired[Optional[List[str]]],
+        "tags": NotRequired[Optional[List[str]]],
+    },
+)
+JsonTestCollectionDefCollectionElementDict = TypedDict(
+    "JsonTestCollectionDefCollectionElementDict",
+    {
+        "identifier": str,
+        "class": Literal["Collection"],
+        "collection_type": str,
+        "elements": NotRequired[Optional[List[JsonTestCollectionDefElementDict]]],
+    },
+)
+JsonTestCollectionDefDict = TypedDict(
+    "JsonTestCollectionDefDict",
+    {
+        "class": Literal["Collection"],
+        "collection_type": str,
+        "elements": NotRequired[Optional[List[JsonTestCollectionDefElementDict]]],
+        "name": NotRequired[Optional[str]],
+    },
+)
+
+
+def xml_data_input_to_json(xml_input: ToolSourceTestInput) -> "JsonTestDatasetDefDict":
+    attributes = xml_input["attributes"]
+    as_dict: JsonTestDatasetDefDict = {}
+    as_dict["class"] = "File"
+    value = xml_input["value"]
+    if value:
+        as_dict["path"] = value
+    _copy_if_exists(attributes, as_dict, "location")
+    _copy_if_exists(attributes, as_dict, "dbkey")
+    _copy_if_exists(attributes, as_dict, "ftype", "filetype")
+    _copy_if_exists(attributes, as_dict, "composite_data", only_if_value=True)
+    tags = attributes.get("tags")
+    if tags:
+        as_dict["tags"] = [t.strip() for t in tags.split(",")]
+    return as_dict
+
+
+def _copy_if_exists(attributes, as_dict, name: str, as_name: Optional[str] = None, only_if_value: bool = False):
+    if name in attributes:
+        value = attributes[name]
+        if not value and only_if_value:
+            return
+        if as_name is None:
+            as_name = name
+        as_dict[as_name] = value
+
+
 class TestCollectionDef:
     __test__ = False  # Prevent pytest from discovering this class (issue #12071)
 
@@ -577,7 +661,33 @@ def __init__(self, attrib, name, collection_type, elements):
         self.elements = elements
         self.name = name
 
-    def to_dict(self) -> TestCollectionDefDict:
+    def _test_format_to_dict(self) -> "JsonTestCollectionDefDict":
+
+        def to_element(xml_element_dict: "TestCollectionDefElementDict") -> "JsonTestCollectionDefElementDict":
+            identifier = xml_element_dict["element_identifier"]
+            element_object = xml_element_dict["element_definition"]
+            if isinstance(element_object, TestCollectionDef):
+                as_dict = element_object._test_format_to_dict()
+                as_dict["identifier"] = identifier
+            else:
+                as_dict = xml_data_input_to_json(element_object)
+                as_dict["identifier"] = identifier
+            return as_dict
+
+        test_format_dict = {
+            "class": "Collection",
+            "elements": list(map(to_element, self.elements)),
+            "collection_type": self.collection_type,
+        }
+        return test_format_dict
+
+    def test_format_to_dict(self) -> JsonTestCollectionDefDict:
+        test_format_dict = self._test_format_to_dict()
+        if self.name:
+            test_format_dict["name"] = self.name
+        return test_format_dict
+
+    def to_dict(self) -> XmlTestCollectionDefDict:
         def element_to_dict(element_dict):
             element_identifier, element_def = element_dict["element_identifier"], element_dict["element_definition"]
             if isinstance(element_def, TestCollectionDef):
@@ -596,23 +706,48 @@ def element_to_dict(element_dict):
         }
 
     @staticmethod
-    def from_dict(as_dict: TestCollectionDefDict):
-        assert as_dict["model_class"] == "TestCollectionDef"
-
-        def element_from_dict(element_dict):
-            if "element_definition" not in element_dict:
-                raise Exception(f"Invalid element_dict {element_dict}")
-            element_def = element_dict["element_definition"]
-            if element_def.get("model_class", None) == "TestCollectionDef":
-                element_def = TestCollectionDef.from_dict(element_def)
-            return {"element_identifier": element_dict["element_identifier"], "element_definition": element_def}
-
-        return TestCollectionDef(
-            attrib=as_dict["attributes"],
-            name=as_dict["name"],
-            elements=list(map(element_from_dict, as_dict["elements"] or [])),
-            collection_type=as_dict["collection_type"],
-        )
+    def from_dict(as_dict: AnyTestCollectionDefDict) -> "TestCollectionDef":
+        if "model_class" in as_dict:
+            xml_as_dict = cast(XmlTestCollectionDefDict, as_dict)
+            assert xml_as_dict["model_class"] == "TestCollectionDef"
+
+            def element_from_dict(element_dict):
+                if "element_definition" not in element_dict:
+                    raise Exception(f"Invalid element_dict {element_dict}")
+                element_def = element_dict["element_definition"]
+                if element_def.get("model_class", None) == "TestCollectionDef":
+                    element_def = TestCollectionDef.from_dict(element_def)
+                return {"element_identifier": element_dict["element_identifier"], "element_definition": element_def}
+
+            return TestCollectionDef(
+                attrib=xml_as_dict["attributes"],
+                name=xml_as_dict["name"],
+                elements=list(map(element_from_dict, xml_as_dict["elements"] or [])),
+                collection_type=xml_as_dict["collection_type"],
+            )
+        else:
+            json_as_dict = cast(JsonTestCollectionDefDict, as_dict)
+
+            def element_from_dict_json(
+                element_dict: JsonTestCollectionDefElementDict,
+            ) -> TestCollectionDefElementObject:
+                element_class = element_dict.get("class")
+                identifier = element_dict["identifier"]
+                if element_class == "Collection":
+                    element_def = TestCollectionDef.from_dict(element_dict)
+                else:
+                    value = element_dict["path"]  # todo handle location
+                    name = element_dict.get("name")
+                    element_def = {"name": name, "value": value, "attributes": {}}
+                return {"element_identifier": identifier, "element_definition": element_def}
+
+            elements = list(map(element_from_dict_json, json_as_dict.get("elements", [])))
+            return TestCollectionDef(
+                attrib={},
+                name=json_as_dict.get("name") or "Unnamed Collection",
+                elements=elements,
+                collection_type=xml_as_dict["collection_type"],
+            )
 
     def collect_inputs(self):
         inputs = []

lib/galaxy/tool_util/parser/xml.py

@@ -45,7 +45,6 @@
     PageSource,
     PagesSource,
     RequiredFiles,
-    TestCollectionDefDict,
     TestCollectionDefElementDict,
     TestCollectionDefElementObject,
     TestCollectionOutputDef,
@@ -58,6 +57,7 @@
     ToolSourceTestOutputAttributes,
     ToolSourceTestOutputs,
     ToolSourceTests,
+    XmlTestCollectionDefDict,
     XrefDict,
 )
 from .output_actions import ToolOutputActionGroup
@@ -1001,7 +1001,7 @@ def __parse_inputs_elems(test_elem, i) -> ToolSourceTestInputs:
     return raw_inputs
 
 
-def _test_collection_def_dict(elem: Element) -> TestCollectionDefDict:
+def _test_collection_def_dict(elem: Element) -> XmlTestCollectionDefDict:
     elements: List[TestCollectionDefElementDict] = []
     attrib: Dict[str, Any] = _element_to_dict(elem)
     collection_type = attrib["type"]
@@ -1017,7 +1017,7 @@ def _test_collection_def_dict(elem: Element) -> TestCollectionDefDict:
             element_definition = __parse_param_elem(element)
         elements.append({"element_identifier": element_identifier, "element_definition": element_definition})
 
-    return TestCollectionDefDict(
+    return XmlTestCollectionDefDict(
         model_class="TestCollectionDef",
         attributes=attrib,
         collection_type=collection_type,

lib/galaxy/tool_util/verify/interactor.py

@@ -38,10 +38,10 @@
 from galaxy.tool_util.parser.interface import (
     AssertionList,
     TestCollectionDef,
-    TestCollectionDefDict,
     TestCollectionOutputDef,
     TestSourceTestOutputColllection,
     ToolSourceTestOutputs,
+    XmlTestCollectionDefDict,
 )
 from galaxy.util import requests
 from galaxy.util.bunch import Bunch
@@ -1754,7 +1754,7 @@ 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"):
-            collection_def_dict = cast(TestCollectionDefDict, value)
+            collection_def_dict = cast(XmlTestCollectionDefDict, value)
             loaded_inputs[key] = TestCollectionDef.from_dict(collection_def_dict)
         else:
             loaded_inputs[key] = value