Don't load custom tools into toolbox

Author: mvdbeek

lib/galaxy/managers/landing.py

@@ -68,7 +68,7 @@ def create_tool_landing_request(self, payload: CreateToolLandingRequestPayload,
         request_state = payload.request_state
 
         ref = ToolRunReference(tool_id=tool_id, tool_version=tool_version, tool_uuid=None)
-        tool = get_tool_from_toolbox(self.app.toolbox, ref)
+        tool = get_tool_from_toolbox(self.app.toolbox, ref, user=None)
         landing_request_state = LandingRequestToolState(request_state or {})
         # Okay this is a hack until tool request API commit is merged, tools don't yet have a parameter
         # schema - so we can't do this properly.

lib/galaxy/managers/tools.py

@@ -24,10 +24,12 @@
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.model import (
     DynamicTool,
+    User,
     UserDynamicToolAssociation,
 )
 from galaxy.tool_util.cwl import tool_proxy
 from galaxy.tool_util.parser.yaml import YamlToolSource
+from galaxy.tool_util.toolbox import AbstractToolBox
 from galaxy.tool_util_models.dynamic_tool_models import (
     DynamicToolPayload,
     DynamicUnprivilegedToolCreatePayload,
@@ -61,17 +63,13 @@ class ToolRunReference(NamedTuple):
 
 
 def get_tool_from_trans(trans: ProvidesUserContext, tool_ref: ToolRunReference) -> Tool:
-    return get_tool_from_toolbox(trans.app.toolbox, tool_ref)
+    return get_tool_from_toolbox(trans.app.toolbox, tool_ref, trans.user)
 
 
-def get_tool_from_toolbox(toolbox, tool_ref: ToolRunReference) -> Tool:
-    get_kwds = dict(
-        tool_id=tool_ref.tool_id,
-        tool_uuid=tool_ref.tool_uuid,
-        tool_version=tool_ref.tool_version,
+def get_tool_from_toolbox(toolbox: AbstractToolBox, tool_ref: ToolRunReference, user: Optional[User]) -> Tool:
+    tool = toolbox.get_tool(
+        tool_id=tool_ref.tool_id, tool_uuid=tool_ref.tool_uuid, tool_version=tool_ref.tool_version, user=user
     )
-
-    tool = toolbox.get_tool(**get_kwds)
     if not tool:
         log.debug(f"Not found tool with kwds [{tool_ref}]")
         raise exceptions.ToolMissingException("Tool not found.")
@@ -102,7 +100,7 @@ def get_tool_by_id_or_uuid(self, id_or_uuid: Union[int, str]) -> Union[DynamicTo
             return self.get_tool_by_uuid(id_or_uuid)
 
     def get_tool_by_uuid(self, uuid: Optional[Union[UUID, str]]):
-        stmt = select(DynamicTool).where(DynamicTool.uuid == uuid)
+        stmt = select(DynamicTool).where(DynamicTool.uuid == uuid, DynamicTool.public == true())
         return self.session().scalars(stmt).one_or_none()
 
     def get_tool_by_tool_id(self, tool_id):

lib/galaxy/tool_util/toolbox/base.py

@@ -412,7 +412,7 @@ def panel_has_tool(self, tool: "Tool", panel_view_id: str) -> bool:
         return panel_view_rendered.has_item_recursive(tool)
 
     def load_dynamic_tool(self, dynamic_tool: "DynamicTool") -> Union["Tool", None]:
-        if not dynamic_tool.active:
+        if not dynamic_tool.active or not dynamic_tool.public:
             return None
 
         tool = self.create_dynamic_tool(dynamic_tool)

test/unit/app/managers/test_landing.py

@@ -54,7 +54,7 @@ def toolbox(self):
 
 class MockToolbox:
 
-    def get_tool(self, tool_id, tool_uuid, tool_version):
+    def get_tool(self, tool_id, tool_uuid, tool_version, user):
         return MockTool()