Merge pull request #18889 from jmchilton/collection_type_check

Improvements to Planemo test format based on feedback/discussions.

lib/galaxy/tool_util/models.py

@@ -13,12 +13,16 @@
 )
 
 from pydantic import (
+    AfterValidator,
     AnyUrl,
     BaseModel,
     ConfigDict,
+    Field,
     RootModel,
 )
 from typing_extensions import (
+    Annotated,
+    Literal,
     NotRequired,
     TypedDict,
 )
@@ -113,7 +117,7 @@ class BaseTestOutputModel(StrictModel):
 
 
 class TestDataOutputAssertions(BaseTestOutputModel):
-    pass
+    class_: Optional[Literal["File"]] = Field("File", alias="class")
 
 
 class TestCollectionCollectionElementAssertions(StrictModel):
@@ -131,14 +135,29 @@ class TestCollectionDatasetElementAssertions(BaseTestOutputModel):
 TestCollectionCollectionElementAssertions.model_rebuild()
 
 
+def _check_collection_type(v: str) -> str:
+    if len(v) == 0:
+        raise ValueError("Invalid empty collection_type specified.")
+    collection_levels = v.split(":")
+    for collection_level in collection_levels:
+        if collection_level not in ["list", "paired"]:
+            raise ValueError(f"Invalid collection_type specified [{v}]")
+    return v
+
+
+CollectionType = Annotated[Optional[str], AfterValidator(_check_collection_type)]
+
+
 class CollectionAttributes(StrictModel):
-    collection_type: Optional[str] = None
+    collection_type: CollectionType = None
 
 
 class TestCollectionOutputAssertions(StrictModel):
+    class_: Optional[Literal["Collection"]] = Field("Collection", alias="class")
     elements: Optional[Dict[str, TestCollectionElementAssertion]] = None
     element_tests: Optional[Dict[str, "TestCollectionElementAssertion"]] = None
     attributes: Optional[CollectionAttributes] = None
+    collection_type: CollectionType = None
 
 
 TestOutputLiteral = Union[bool, int, float, str]

lib/galaxy/tool_util/parser/interface.py

@@ -870,6 +870,19 @@ def from_dict(as_dict):
             element_tests=as_dict["element_tests"],
         )
 
+    @staticmethod
+    def from_yaml_test_format(as_dict):
+        if "attributes" not in as_dict:
+            as_dict["attributes"] = {}
+        attributes = as_dict["attributes"]
+        # setup preferred name "elements" in accordance with work in https://github.com/galaxyproject/planemo/pull/1417
+        # TODO: test this works recursively...
+        if "elements" in as_dict and "element_tests" not in as_dict:
+            as_dict["element_tests"] = as_dict["elements"]
+        if "collection_type" in as_dict:
+            attributes["type"] = as_dict["collection_type"]
+        return TestCollectionOutputDef.from_dict(as_dict)
+
     def to_dict(self):
         return dict(name=self.name, attributes=self.attrib, element_tests=self.element_tests)
 

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

@@ -9,6 +9,8 @@
     filter_file: i1
   outputs:
     output:
+      class: Collection
+      collection_type: list
       elements:
         i1:
           asserts:

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

@@ -3,7 +3,8 @@
   job: {}
   outputs:
     out:
-      attributes: {collection_type: 'list'}
+      class: Collection
+      collection_type: list
       elements:
         'oe1-ie1':
           asserts:

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

@@ -8,6 +8,8 @@
           content: "0 mycoolline\n1 mysecondline\n"
   outputs:
     out:
+      class: Collection
+      collection_type: list
       elements:
         'samp1-0':
           asserts:

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

@@ -10,6 +10,7 @@
       type: raw
   outputs:
     output:
+      class: File
       asserts:
         - that: has_line
           line: "parameter: 2"

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

@@ -10,7 +10,8 @@
           content: B
   outputs:
     out1:
-      attributes: { collection_type: list }
+      class: Collection
+      collection_type: list
       elements:
         A:
           asserts:

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

@@ -16,6 +16,8 @@
           ext: 'expression.json'
   outputs:
     output:
+      class: Collection
+      collection_type: list
       elements:
         the_example_2:
           asserts:

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

@@ -10,6 +10,7 @@
       type: raw
   outputs:
     output:
+      class: File
       asserts:
         - that: has_text
           text: "col 1,2"

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

@@ -9,6 +9,7 @@
       type: raw
   outputs:
     output:
+      class: File
       asserts:
         - that: has_line
           line: '--ex1,ex2,--ex3'

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

@@ -6,12 +6,14 @@
       type: raw
   outputs:
     output_1:
+      class: File
       asserts:
         - that: has_text
           text: 'Version 0.1'
         - that: not_has_text
           text: 'Version 0.2'
     output_2:
+      class: File
       asserts:
         - that: has_text
           text: 'Version 0.2'

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

@@ -18,5 +18,6 @@
           type: File
   outputs:
     output:
+      class: File
       metadata:
         name: 'the_dataset_pair suffix'

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

@@ -5,8 +5,10 @@
       replaceme: moocow
   outputs:
     out1:
+      class: File
       metadata:
         name: 'moocow name'
     out2:
+      class: File
       metadata:
         name: 'moocow name 2'

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

@@ -6,8 +6,10 @@
       type: raw
   outputs:
     out1:
+      class: File
       metadata:
         name: 'moocow name'
     out2:
+      class: File
       metadata:
         name: 'moocow name 2'

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

@@ -6,8 +6,10 @@
       type: raw
   outputs:
     out1:
+      class: File
       metadata:
         name: 'moocow name'
     out2:
+      class: File
       metadata:
         name: 'moocow name 2'

lib/galaxy_test/workflow/tests.py

@@ -96,10 +96,7 @@ def verify_dataset(dataset: dict, test_properties: OutputChecks):
         if is_collection_test:
             assert isinstance(test_properties, dict)
             test_properties["name"] = output_name
-            # setup preferred name "elements" in accordance with work in https://github.com/galaxyproject/planemo/pull/1417
-            test_properties["element_tests"] = test_properties["elements"]
-            output_def = TestCollectionOutputDef.from_dict(test_properties)
-
+            output_def = TestCollectionOutputDef.from_yaml_test_format(test_properties)
             invocation_details = self.workflow_populator.get_invocation(run_summary.invocation_id, step_details=True)
             assert output_name in invocation_details["output_collections"]
             test_output = invocation_details["output_collections"][output_name]