Fix typing

lib/galaxy/schema/invocation.py

@@ -343,21 +343,34 @@ class InvocationStep(Model, WithModelClass):
     model_class: INVOCATION_STEP_MODEL_CLASS = ModelClassField(INVOCATION_STEP_MODEL_CLASS)
     id: Annotated[EncodedDatabaseIdField, Field(..., title="Invocation Step ID")]
     update_time: Optional[datetime] = schema.UpdateTimeField
-    job_id: Optional[EncodedDatabaseIdField] = Field(
-        default=None,
-        title="Job ID",
-        description="The encoded ID of the job associated with this workflow invocation step.",
-    )
-    workflow_step_id: EncodedDatabaseIdField = Field(
-        ...,
-        title="Workflow step ID",
-        description="The encoded ID of the workflow step associated with this workflow invocation step.",
-    )
-    subworkflow_invocation_id: Optional[EncodedDatabaseIdField] = Field(
-        default=None,
-        title="Subworkflow invocation ID",
-        description="The encoded ID of the subworkflow invocation.",
-    )
+    job_id: Optional[
+        Annotated[
+            EncodedDatabaseIdField,
+            Field(
+                default=None,
+                title="Job ID",
+                description="The encoded ID of the job associated with this workflow invocation step.",
+            ),
+        ]
+    ]
+    workflow_step_id: Annotated[
+        EncodedDatabaseIdField,
+        Field(
+            ...,
+            title="Workflow step ID",
+            description="The encoded ID of the workflow step associated with this workflow invocation step.",
+        ),
+    ]
+    subworkflow_invocation_id: Optional[
+        Annotated[
+            EncodedDatabaseIdField,
+            Field(
+                default=None,
+                title="Subworkflow invocation ID",
+                description="The encoded ID of the subworkflow invocation.",
+            ),
+        ]
+    ]
     state: Optional[Union[InvocationStepState, JobState]] = Field(
         default=None,
         title="State of the invocation step",

lib/galaxy/schema/schema.py

@@ -1429,18 +1429,14 @@ class InvocationSortByEnum(str, Enum):
 
 
 class InvocationIndexQueryPayload(Model):
-    workflow_id: Optional[DecodedDatabaseIdField] = Field(
+    workflow_id: Optional[int] = Field(
         None, title="Workflow ID", description="Return only invocations for this Workflow ID"
     )
-    history_id: Optional[DecodedDatabaseIdField] = Field(
+    history_id: Optional[int] = Field(
         None, title="History ID", description="Return only invocations for this History ID"
     )
-    job_id: Optional[DecodedDatabaseIdField] = Field(
-        None, title="Job ID", description="Return only invocations for this Job ID"
-    )
-    user_id: Optional[DecodedDatabaseIdField] = Field(
-        None, title="User ID", description="Return invocations for this User ID"
-    )
+    job_id: Optional[int] = Field(None, title="Job ID", description="Return only invocations for this Job ID")
+    user_id: Optional[int] = Field(None, title="User ID", description="Return invocations for this User ID")
     sort_by: Optional[InvocationSortByEnum] = Field(
         None, title="Sort By", description="Sort Workflow Invocations by this attribute"
     )

lib/galaxy/webapps/galaxy/api/common.py

@@ -153,7 +153,7 @@ def parse_serialization_params(
 
 
 def query_serialization_params(
-    view: Annotated[Optional[str], SerializationViewQueryParam] = None,
+    view: SerializationViewQueryParam = None,
     keys: Optional[str] = SerializationKeysQueryParam,
 ) -> SerializationParams:
     return parse_serialization_params(view=view, keys=keys)

lib/galaxy/webapps/galaxy/api/configuration.py

@@ -11,7 +11,6 @@
 )
 
 from fastapi import Path
-from typing_extensions import Annotated
 
 from galaxy.managers.configuration import ConfigurationManager
 from galaxy.managers.context import ProvidesUserContext
@@ -61,7 +60,7 @@ def whoami(self, trans: ProvidesUserContext = DependsOnTrans) -> Optional[UserMo
     def index(
         self,
         trans: ProvidesUserContext = DependsOnTrans,
-        view: Annotated[Optional[str], SerializationViewQueryParam] = None,
+        view: SerializationViewQueryParam = None,
         keys: Optional[str] = SerializationKeysQueryParam,
     ) -> Dict[str, Any]:
         """

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -56,7 +56,6 @@
     InvocationMessageResponseModel,
     InvocationReport,
     InvocationSerializationParams,
-    InvocationSerializationView,
     InvocationStep,
     InvocationStepJobsResponseCollectionJobsModel,
     InvocationStepJobsResponseJobModel,
@@ -1122,8 +1121,8 @@ def undelete_workflow(
     )
     def show_versions(
         self,
+        workflow_id: StoredWorkflowIDPathParam,
         trans: ProvidesUserContext = DependsOnTrans,
-        workflow_id: DecodedDatabaseIdField = StoredWorkflowIDPathParam,
         instance: Annotated[Optional[bool], InstanceQueryParam] = False,
     ):
         return self.service.get_versions(trans, workflow_id, instance)
@@ -1278,7 +1277,7 @@ class FastAPIInvocations:
     )
     def create_invocations_from_store(
         self,
-        payload: Annotated[CreateInvocationsFromStorePayload, CreateInvocationsFromStoreBody],
+        payload: CreateInvocationsFromStoreBody,
         trans: ProvidesHistoryContext = DependsOnTrans,
     ) -> List[WorkflowInvocationResponse]:
         """
@@ -1299,18 +1298,18 @@ def create_invocations_from_store(
     def index_invocations(
         self,
         response: Response,
-        workflow_id: Annotated[Optional[DecodedDatabaseIdField], WorkflowIdQueryParam] = None,
-        history_id: Annotated[Optional[DecodedDatabaseIdField], HistoryIdQueryParam] = None,
-        job_id: Annotated[Optional[DecodedDatabaseIdField], JobIdQueryParam] = None,
-        user_id: Annotated[Optional[DecodedDatabaseIdField], UserIdQueryParam] = None,
-        sort_by: Annotated[Optional[InvocationSortByEnum], InvocationsSortByQueryParam] = None,
-        sort_desc: Annotated[Optional[bool], InvocationsSortDescQueryParam] = False,
-        include_terminal: Annotated[Optional[bool], InvocationsIncludeTerminalQueryParam] = True,
-        limit: Annotated[Optional[int], InvocationsLimitQueryParam] = None,
-        offset: Annotated[Optional[int], InvocationsOffsetQueryParam] = None,
-        instance: Annotated[Optional[bool], InvocationsInstanceQueryParam] = False,
-        view: Annotated[Optional[InvocationSerializationView], SerializationViewQueryParam] = None,
-        step_details: Annotated[Optional[bool], StepDetailQueryParam] = False,
+        workflow_id: WorkflowIdQueryParam = None,
+        history_id: HistoryIdQueryParam = None,
+        job_id: JobIdQueryParam = None,
+        user_id: UserIdQueryParam = None,
+        sort_by: InvocationsSortByQueryParam = None,
+        sort_desc: InvocationsSortDescQueryParam = False,
+        include_terminal: InvocationsIncludeTerminalQueryParam = True,
+        limit: InvocationsLimitQueryParam = None,
+        offset: InvocationsOffsetQueryParam = None,
+        instance: InvocationsInstanceQueryParam = False,
+        view: SerializationViewQueryParam = None,
+        step_details: StepDetailQueryParam = False,
         trans: ProvidesUserContext = DependsOnTrans,
     ) -> List[WorkflowInvocationResponse]:
         """If workflow_id is supplied (either via URL or query parameter) it should be an
@@ -1322,17 +1321,17 @@ def index_invocations(
         :raises: exceptions.MessageException, exceptions.ObjectNotFound
         """
         invocation_payload = InvocationIndexPayload(
+            workflow_id=workflow_id,
+            history_id=history_id,
+            job_id=job_id,
+            user_id=user_id,
             sort_by=sort_by,
             sort_desc=sort_desc,
             include_terminal=include_terminal,
             limit=limit,
             offset=offset,
             instance=instance,
         )
-        invocation_payload.workflow_id = workflow_id
-        invocation_payload.history_id = history_id
-        invocation_payload.job_id = job_id
-        invocation_payload.user_id = user_id
         serialization_params = InvocationSerializationParams(
             view=view,
             step_details=step_details,
@@ -1349,18 +1348,18 @@ def index_invocations(
     def index_workflow_invocations(
         self,
         response: Response,
-        workflow_id: Annotated[DecodedDatabaseIdField, StoredWorkflowIDPathParam],
-        history_id: Annotated[Optional[DecodedDatabaseIdField], HistoryIdQueryParam] = None,
-        job_id: Annotated[Optional[DecodedDatabaseIdField], JobIdQueryParam] = None,
-        user_id: Annotated[Optional[DecodedDatabaseIdField], UserIdQueryParam] = None,
-        sort_by: Annotated[Optional[InvocationSortByEnum], InvocationsSortByQueryParam] = None,
-        sort_desc: Annotated[Optional[bool], InvocationsSortDescQueryParam] = False,
-        include_terminal: Annotated[Optional[bool], InvocationsIncludeTerminalQueryParam] = True,
-        limit: Annotated[Optional[int], InvocationsLimitQueryParam] = None,
-        offset: Annotated[Optional[int], InvocationsOffsetQueryParam] = None,
-        instance: Annotated[Optional[bool], InvocationsInstanceQueryParam] = False,
-        view: Annotated[Optional[InvocationSerializationView], SerializationViewQueryParam] = None,
-        step_details: Annotated[Optional[bool], StepDetailQueryParam] = False,
+        workflow_id: StoredWorkflowIDPathParam,
+        history_id: HistoryIdQueryParam = None,
+        job_id: JobIdQueryParam = None,
+        user_id: UserIdQueryParam = None,
+        sort_by: InvocationsSortByQueryParam = None,
+        sort_desc: InvocationsSortDescQueryParam = False,
+        include_terminal: InvocationsIncludeTerminalQueryParam = True,
+        limit: InvocationsLimitQueryParam = None,
+        offset: InvocationsOffsetQueryParam = None,
+        instance: InvocationsInstanceQueryParam = False,
+        view: SerializationViewQueryParam = None,
+        step_details: StepDetailQueryParam = False,
         trans: ProvidesUserContext = DependsOnTrans,
     ) -> List[WorkflowInvocationResponse]:
         """An alias for GET '/api/invocations'"""