Rename ToolResponse model and only use it in execute operation of the…

… tool API

lib/galaxy/schema/tools.py

@@ -137,7 +137,7 @@ class HDCADetailedWithOutputName(HDCADetailed):
 AnyHDCAWithOutputName = Union[HDCADetailedWithOutputName, HDCASummaryWithOutputName]
 
 
-class ToolResponse(Model):
+class ExecuteToolResponse(Model):
     outputs: List[AnyHDAWithOutputName] = Field(
         default=[],
         title="Outputs",

lib/galaxy/webapps/galaxy/api/tools.py

@@ -33,7 +33,7 @@
 )
 from galaxy.schema.tools import (
     ExecuteToolPayload,
-    ToolResponse,
+    ExecuteToolResponse,
 )
 from galaxy.tools.evaluation import global_tool_errors
 from galaxy.util.zipstream import ZipstreamWrapper
@@ -80,9 +80,7 @@ class FetchTools:
     service: ToolsService = depends(ToolsService)
 
     @router.post("/api/tools/fetch", summary="Upload files to Galaxy", route_class_override=JsonApiRoute)
-    async def fetch_json(
-        self, payload: FetchDataPayload = Body(...), trans: ProvidesHistoryContext = DependsOnTrans
-    ) -> ToolResponse:
+    async def fetch_json(self, payload: FetchDataPayload = Body(...), trans: ProvidesHistoryContext = DependsOnTrans):
         return self.service.create_fetch(trans, payload)
 
     @router.post(
@@ -96,7 +94,7 @@ async def fetch_form(
         payload: FetchDataFormPayload = Depends(FetchDataForm.as_form),
         files: Optional[List[UploadFile]] = None,
         trans: ProvidesHistoryContext = DependsOnTrans,
-    ) -> ToolResponse:
+    ):
         files2: List[StarletteUploadFile] = cast(List[StarletteUploadFile], files or [])
 
         # FastAPI's UploadFile is a very light wrapper around starlette's UploadFile
@@ -115,7 +113,7 @@ def execute(
         self,
         payload: ExecuteToolPayload = depend_on_either_json_or_form_data(ExecuteToolPayload),
         trans: ProvidesHistoryContext = DependsOnTrans,
-    ) -> ToolResponse:
+    ) -> ExecuteToolResponse:
         return self.service.execute(trans, payload)
 
 

lib/galaxy/webapps/galaxy/services/tools.py

@@ -36,7 +36,7 @@
 )
 from galaxy.schema.tools import (
     ExecuteToolPayload,
-    ToolResponse,
+    ExecuteToolResponse,
 )
 from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.tools import Tool
@@ -98,7 +98,7 @@ def create_fetch(
         trans: ProvidesHistoryContext,
         fetch_payload: Union[FetchDataFormPayload, FetchDataPayload],
         files: Optional[List[UploadFile]] = None,
-    ) -> ToolResponse:
+    ):
         payload = fetch_payload.model_dump(exclude_unset=True)
         request_version = "1"
         history_id = payload.pop("history_id")
@@ -132,7 +132,7 @@ def execute(
         self,
         trans: ProvidesHistoryContext,
         payload: ExecuteToolPayload,
-    ) -> ToolResponse:
+    ) -> ExecuteToolResponse:
         tool_id = payload.tool_id
         tool_uuid = payload.tool_uuid
         if tool_id in PROTECTED_TOOLS:
@@ -149,13 +149,14 @@ def execute(
             if key.startswith("files_") and isinstance(create_payload[key], UploadFile):
                 files[key] = self.create_temp_file_execute(trans, create_payload.pop(key))
         create_payload.update(files)
-        return self._create(trans, create_payload)
+        return self._create(trans, create_payload, encode_ids=False)
 
     def _create(
         self,
         trans: ProvidesHistoryContext,
         payload: Dict[str, Any],
-    ) -> ToolResponse:
+        encode_ids: bool = True,
+    ):
         if trans.user_is_bootstrap_admin:
             raise exceptions.RealUserRequiredException("Only real users can execute tools or run jobs.")
         action = payload.get("action")
@@ -249,9 +250,9 @@ def _create(
             with transaction(trans.sa_session):
                 trans.sa_session.commit()
 
-        return self._handle_inputs_output_to_api_response(trans, tool, target_history, vars)
+        return self._handle_inputs_output_to_api_response(trans, tool, target_history, vars, encode_ids)
 
-    def _handle_inputs_output_to_api_response(self, trans, tool, target_history, vars) -> ToolResponse:
+    def _handle_inputs_output_to_api_response(self, trans, tool, target_history, vars, encode_ids=True):
         # TODO: check for errors and ensure that output dataset(s) are available.
         output_datasets = vars.get("out_data", [])
         rval: Dict[str, Any] = {"outputs": [], "output_collections": [], "jobs": [], "implicit_collections": []}
@@ -270,6 +271,9 @@ def _handle_inputs_output_to_api_response(self, trans, tool, target_history, var
             output_dict["output_name"] = output_name
             outputs.append(output_dict)
 
+        for job in vars.get("jobs", []):
+            rval["jobs"].append(job.to_dict(view="collection"))
+
         for output_name, collection_instance in vars.get("output_collections", []):
             history = target_history or trans.history
             output_dict = dictify_dataset_collection_instance(
@@ -292,11 +296,10 @@ def _handle_inputs_output_to_api_response(self, trans, tool, target_history, var
             output_dict["output_name"] = output_name
             rval["implicit_collections"].append(output_dict)
 
-        # Encoding the job ids is handled by the pydantic model
-        for job in vars.get("jobs", []):
-            rval["jobs"].append(job.to_dict(view="collection"))
+        if encode_ids:
+            rval = self.encode_all_ids(rval, recursive=True)
 
-        return ToolResponse(**rval)
+        return rval
 
     def _search(self, q, view):
         """