Unverified Commit eb823365 authored by mvdbeek's avatar mvdbeek
Browse files

Don't load custom tools into toolbox

parent ba5122a7

lib/galaxy/managers/landing.py

+1 −1
Original line number Diff line number Diff line
@@ -68,7 +68,7 @@ class LandingRequestManager: 
        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

+7 −9
Original line number Diff line number Diff line
@@ -24,10 +24,12 @@ from galaxy import ( 
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 @@ class DynamicToolManager(ModelManager[DynamicTool]): 
            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

+1 −1
Original line number Diff line number Diff line
@@ -412,7 +412,7 @@ class AbstractToolBox(ManagesIntegratedToolPanelMixin): 
        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

+1 −1
Original line number Diff line number Diff line
@@ -54,7 +54,7 @@ class MockApp: 


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()