mypy fixes...

dddd h dear...
jmchilton · Sep 10, 2024 · 869620f · 869620f
1 parent 669c65c
commit 869620f
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Showing 4 changed files with 20 additions and 20 deletions.
diff --git a/lib/galaxy/model/deferred.py b/lib/galaxy/model/deferred.py
@@ -150,14 +150,15 @@ def ensure_materialized(
             except DetachedInstanceError:
                 history = None
 
-        materialized_dataset_instance: Union[HistoryDatasetAssociation, LibraryDatasetDatasetAssociation]
+        materialized_dataset_instance: HistoryDatasetAssociation
         if not in_place:
             materialized_dataset_instance = HistoryDatasetAssociation(
                 create_dataset=False,  # is the default but lets make this really clear...
                 history=history,
             )
         else:
-            materialized_dataset_instance = dataset_instance
+            assert isinstance(dataset_instance, HistoryDatasetAssociation)
+            materialized_dataset_instance = cast(HistoryDatasetAssociation, dataset_instance)
         if attached:
             sa_session = self._sa_session
             if sa_session is None:

diff --git a/lib/galaxy/tool_util/parameters/convert.py b/lib/galaxy/tool_util/parameters/convert.py
@@ -16,7 +16,7 @@
 from .models import (
     DataCollectionRequest,
     DataParameterModel,
-    DataRequest,
+    DataRequestHda,
     DataRequestInternalHda,
     DataRequestUri,
     SelectParameterModel,
@@ -156,7 +156,7 @@ def dereference_callback(parameter: ToolParameterT, value: Any):
 
 # interfaces for adapting test data dictionaries to tool request dictionaries
 # e.g. {class: File, path: foo.bed} => {src: hda, id: ab1235cdfea3}
-AdaptDatasets = Callable[[JsonTestDatasetDefDict], DataRequest]
+AdaptDatasets = Callable[[JsonTestDatasetDefDict], DataRequestHda]
 AdaptCollections = Callable[[JsonTestCollectionDefDict], DataCollectionRequest]
 
 

diff --git a/lib/galaxy/tool_util/parameters/models.py b/lib/galaxy/tool_util/parameters/models.py
@@ -269,18 +269,18 @@ class DataRequestUri(StrictModel):
     deferred: StrictBool = False
 
 
-DataRequest: Type = Annotated[union_type([DataRequestHda, DataRequestLdda, DataRequestUri]), Field(discriminator="src")]
+DataRequest: Type = cast(Type, Annotated[union_type([DataRequestHda, DataRequestLdda, DataRequestUri]), Field(discriminator="src")])
 
 
 class BatchDataInstance(StrictModel):
     src: MultiDataSrcT
     id: StrictStr
 
 
-MultiDataInstance: Type = Annotated[
+MultiDataInstance: Type = cast(Type, Annotated[
     union_type([DataRequestHda, DataRequestLdda, DataRequestHdca, DataRequestUri]), Field(discriminator="src")
-]
-MultiDataRequest: Type = union_type([MultiDataInstance, List[MultiDataInstance]])
+])
+MultiDataRequest: Type = cast(Type, union_type([MultiDataInstance, list_type(MultiDataInstance)]))
 
 
 class DataRequestInternalHda(StrictModel):
@@ -298,12 +298,12 @@ class DataRequestInternalHdca(StrictModel):
     id: StrictInt
 
 
-DataRequestInternal = Annotated[
+DataRequestInternal: Type = cast(Type, Annotated[
     Union[DataRequestInternalHda, DataRequestInternalLdda, DataRequestUri], Field(discriminator="src")
-]
-DataRequestInternalDereferenced = Annotated[
+])
+DataRequestInternalDereferenced: Type = cast(Type, Annotated[
     Union[DataRequestInternalHda, DataRequestInternalLdda], Field(discriminator="src")
-]
+])
 DataJobInternal = DataRequestInternalDereferenced
 
 
@@ -312,17 +312,17 @@ class BatchDataInstanceInternal(StrictModel):
     id: StrictInt
 
 
-MultiDataInstanceInternal = Annotated[
+MultiDataInstanceInternal: Type = cast(Type, Annotated[
     Union[DataRequestInternalHda, DataRequestInternalLdda, DataRequestInternalHdca, DataRequestUri],
     Field(discriminator="src"),
-]
-MultiDataInstanceInternalDereferenced = Annotated[
+])
+MultiDataInstanceInternalDereferenced: Type = cast(Type, Annotated[
     Union[DataRequestInternalHda, DataRequestInternalLdda, DataRequestInternalHdca], Field(discriminator="src")
-]
+])
 
-MultiDataRequestInternal: Type = union_type([MultiDataInstanceInternal, List[MultiDataInstanceInternal]])
+MultiDataRequestInternal: Type = union_type([MultiDataInstanceInternal, list_type(MultiDataInstanceInternal)])
 MultiDataRequestInternalDereferenced: Type = union_type(
-    [MultiDataInstanceInternalDereferenced, List[MultiDataInstanceInternalDereferenced]]
+    [MultiDataInstanceInternalDereferenced, list_type(MultiDataInstanceInternalDereferenced)]
 )
 
 

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
@@ -76,7 +76,6 @@
     input_models_for_pages,
     JobInternalToolState,
     RequestInternalDereferencedToolState,
-    RequestInternalToolState,
     ToolParameterBundle,
 )
 from galaxy.tool_util.parser import (
@@ -1836,7 +1835,7 @@ def visit_inputs(self, values, callback):
     def expand_incoming_async(
         self,
         request_context: WorkRequestContext,
-        tool_request_internal_state: RequestInternalToolState,
+        tool_request_internal_state: RequestInternalDereferencedToolState,
         rerun_remap_job_id: Optional[int],
     ) -> Tuple[
         List[ToolStateJobInstancePopulatedT],