Type the agents stack for the context it actually receives

The agents stack declared trans as ProvidesUserContext everywhere, so
reaching the toolbox panel views needed a cast back to
SessionRequestContext. Nothing was ever narrower: DependsOnTrans is
declared to return a SessionRequestContext, and the MCP entry point builds
one explicitly, so the declarations were widening what callers hand over.

Declare SessionRequestContext along that chain instead, from the endpoints
through AgentService and GalaxyAgentDependencies to
AgentOperationsManager, and drop the cast. This also makes the toolbox
search attribute resolve, so its type: ignore goes too.

lib/galaxy/agents/base.py

@@ -29,13 +29,13 @@ from typing import (
 import yaml
 
 from galaxy.exceptions import ConfigurationError
-from galaxy.managers.context import ProvidesUserContext
 from galaxy.model import User
 from galaxy.schema.agents import (
     ActionSuggestion,
     ActionType,
     ConfidenceLevel,
 )
+from galaxy.work.context import SessionRequestContext
 
 if TYPE_CHECKING:
     from galaxy.config import GalaxyAppConfiguration
@@ -353,7 +353,7 @@ class AgentRunState:
 class GalaxyAgentDependencies:
     """Dependencies passed to Galaxy agents via dependency injection."""
 
-    trans: ProvidesUserContext
+    trans: SessionRequestContext
     user: User
     config: "GalaxyAppConfiguration"
     # Callable to get agent instances, avoids circular import in base.py

lib/galaxy/agents/operations.py

@@ -7,14 +7,12 @@ Delegates to the Galaxy service layer for validation, permission checks, and pag
 import logging
 from typing import (
     Any,
-    cast,
     Literal,
 )
 
 from sqlalchemy import select
 
 from galaxy.agents import iwc
-from galaxy.managers.context import ProvidesUserContext
 from galaxy.managers.hdas import HDAManager
 from galaxy.managers.tools import DynamicToolManager
 from galaxy.model import UserDynamicToolAssociation
@@ -63,7 +61,7 @@ ID_FIELDS = {
 class AgentOperationsManager:
     """Shared operations for AI agents, delegating to Galaxy's service layer."""
 
-    def __init__(self, app: MinimalManagerApp, trans: ProvidesUserContext):
+    def __init__(self, app: MinimalManagerApp, trans: SessionRequestContext):
         self.app = app
         self.trans = trans
         self._tools_service: Any | None = None
@@ -636,13 +634,10 @@ class AgentOperationsManager:
         }
 
     def get_tool_panel(self, view: str | None = None) -> dict[str, Any]:
-        # The agents stack types trans as ProvidesUserContext throughout, but at runtime it is
-        # always the SessionRequestContext the panel-view methods require.
-        trans = cast("SessionRequestContext", self.trans)
         if view is None:
-            view = self.app.toolbox._default_panel_view(trans)
+            view = self.app.toolbox._default_panel_view(self.trans)
 
-        tool_panel = self.app.toolbox.to_panel_view(trans, view=view)
+        tool_panel = self.app.toolbox.to_panel_view(self.trans, view=view)
 
         return {"tool_panel": tool_panel, "view": view}
 

lib/galaxy/agents/tools.py

@@ -246,7 +246,7 @@ class ToolRecommendationAgent(BaseGalaxyAgent):
 
         try:
             panel_view = self.deps.config.default_panel_view or "default"
-            toolbox_search = self.deps.trans.app.toolbox_search  # type: ignore[attr-defined]
+            toolbox_search = self.deps.trans.app.toolbox_search
             tool_ids = toolbox_search.search(query, panel_view, self.deps.config)
 
             tools = []

lib/galaxy/managers/agents.py

@@ -9,10 +9,10 @@ from galaxy.agents import GalaxyAgentDependencies
 from galaxy.agents.registry import AgentRegistry
 from galaxy.agents.router import QueryRouterAgent
 from galaxy.config import GalaxyAppConfiguration
-from galaxy.managers.context import ProvidesUserContext
 from galaxy.managers.jobs import JobManager
 from galaxy.model import User
 from galaxy.schema.agents import AgentResponse
+from galaxy.work.context import SessionRequestContext
 
 log = logging.getLogger(__name__)
 
@@ -30,7 +30,7 @@ class AgentService:
         self.job_manager = job_manager
         self.registry = registry
 
-    def create_dependencies(self, trans: ProvidesUserContext, user: User) -> GalaxyAgentDependencies:
+    def create_dependencies(self, trans: SessionRequestContext, user: User) -> GalaxyAgentDependencies:
         """Create agent dependencies for dependency injection."""
         toolbox = trans.app.toolbox if hasattr(trans, "app") and hasattr(trans.app, "toolbox") else None
         return GalaxyAgentDependencies(
@@ -47,7 +47,7 @@ class AgentService:
         self,
         agent_type: str,
         query: str,
-        trans: ProvidesUserContext,
+        trans: SessionRequestContext,
         user: User,
         context: dict[str, Any] | None = None,
     ) -> AgentResponse:
@@ -96,7 +96,7 @@ class AgentService:
     async def route_and_execute(
         self,
         query: str,
-        trans: ProvidesUserContext,
+        trans: SessionRequestContext,
         user: User,
         context: dict[str, Any] | None = None,
         agent_type: str = "auto",

lib/galaxy/webapps/galaxy/api/agents.py

@@ -30,6 +30,7 @@ from galaxy.webapps.galaxy.api import (
     DependsOnUser,
     Router,
 )
+from galaxy.work.context import SessionRequestContext
 
 log = logging.getLogger(__name__)
 
@@ -90,7 +91,7 @@ class AgentAPI:
     async def query_agent(
         self,
         request: AgentQueryRequest,
-        trans: ProvidesUserContext = DependsOnTrans,
+        trans: SessionRequestContext = DependsOnTrans,
         user: User = DependsOnUser,
     ) -> AgentQueryResponse:
         """Query an AI agent. Use agent_type='auto' for automatic routing.
@@ -129,7 +130,7 @@ class AgentAPI:
         job_id: DecodedDatabaseIdField | None = Body(None, description="Job ID for context"),
         error_details: dict[str, Any] | None = Body(None, description="Additional error details"),
         save_exchange: bool | None = Body(None, description="Save exchange for feedback tracking. Defaults to false."),
-        trans: ProvidesUserContext = DependsOnTrans,
+        trans: SessionRequestContext = DependsOnTrans,
         user: User = DependsOnUser,
     ) -> AgentResponse:
         """Analyze job errors and provide debugging assistance.
@@ -181,7 +182,7 @@ class AgentAPI:
         query: str = Body(..., description="Description of the tool to create"),
         context: dict[str, Any] | None = Body(None, description="Additional context for tool creation"),
         save_exchange: bool | None = Body(None, description="Save exchange for feedback tracking. Defaults to false."),
-        trans: ProvidesUserContext = DependsOnTrans,
+        trans: SessionRequestContext = DependsOnTrans,
         user: User = DependsOnUser,
     ) -> AgentResponse:
         """Create a custom Galaxy tool.
@@ -216,7 +217,7 @@ class AgentAPI:
     async def history_summary(
         self,
         history_id: str = Body(..., embed=True, description="Encoded id of the history to summarize."),
-        trans: ProvidesUserContext = DependsOnTrans,
+        trans: SessionRequestContext = DependsOnTrans,
         user: User = DependsOnUser,
     ) -> AgentResponse:
         """Produce a comprehensive markdown report for a history's analysis.

lib/galaxy/webapps/galaxy/api/chat.py

@@ -28,7 +28,6 @@ from galaxy.exceptions import (
 from galaxy.managers.agents import AgentService
 from galaxy.managers.chat import ChatManager
 from galaxy.managers.context import (
-    ProvidesHistoryContext,
     ProvidesUserContext,
 )
 from galaxy.managers.jobs import JobManager
@@ -53,6 +52,7 @@ from galaxy.webapps.galaxy.api import (
     DependsOnUser,
     Router,
 )
+from galaxy.work.context import SessionRequestContext
 
 # Import agent system
 try:
@@ -132,7 +132,7 @@ class ChatAPI:
         payload: ChatPayload | None = None,
         query: str | None = Query(default=None, description="Query string for general chat"),
         agent_type: str = Query(default="auto", description="Agent type to use for the query"),
-        trans: ProvidesHistoryContext = DependsOnTrans,
+        trans: SessionRequestContext = DependsOnTrans,
         user: User = DependsOnUser,
     ) -> ChatResponse:
         """GalaxyAI endpoint - handles both job-based and general chat queries
@@ -412,7 +412,7 @@ class ChatAPI:
         workflow_id: str = Path(..., description="Workflow ID to generate the report for"),
         version: int | None = Query(None, description="Version of the workflow"),
         instance: bool = Query(False, description="Whether the workflow_id is an instance ID"),
-        trans: ProvidesUserContext = DependsOnTrans,
+        trans: SessionRequestContext = DependsOnTrans,
         user: User = DependsOnUser,
     ) -> WorkflowReportResponse:
         """Generate a report for the specified workflow."""
@@ -566,7 +566,7 @@ class ChatAPI:
         self,
         query: str,
         agent_type: str,
-        trans: ProvidesUserContext,
+        trans: SessionRequestContext,
         user: User,
         job=None,
         context: dict[str, Any] | None = None,
@@ -579,7 +579,7 @@ class ChatAPI:
         self,
         query: str,
         agent_type: str,
-        trans: ProvidesUserContext,
+        trans: SessionRequestContext,
         user: User,
         job=None,
         context: dict[str, Any] | None = None,

test/integration/test_agents.py

@@ -14,6 +14,7 @@ For deterministic tests without LLM, see test_static_agent_backend.py.
 import asyncio
 import logging
 import os
+from typing import cast
 
 import pytest
 from fastmcp import (
@@ -26,6 +27,7 @@ from galaxy.agents.operations import AgentOperationsManager
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.util.unittest_utils import pytestmark_live_llm
 from galaxy.webapps.galaxy.api.mcp import get_mcp_app
+from galaxy.work.context import SessionRequestContext
 from galaxy_test.base.populators import (
     DatasetPopulator,
     TOOL_WITH_SHELL_COMMAND,
@@ -216,7 +218,8 @@ class TestAgentOperationsManagerEncoding(AgentIntegrationTestCase):
             def user_is_admin(self):
                 return False
 
-        trans = MinimalTrans(self._app)
+        # the double only needs security.encode_id for _encode_ids_in_response
+        trans = cast(SessionRequestContext, MinimalTrans(self._app))
         return AgentOperationsManager(app=self._app, trans=trans)
 
     def test_encode_ids_helper_encodes_nested_ids(self):