Unverified Commit 3a195be3 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #19335 from mvdbeek/nested_subworkflow_import_fix 

[24.1] Fix importing shared workflows with deeply nested subworkflows
parents 2ca8678b 2406c879

lib/galaxy/model/__init__.py

+7 −7
Original line number Diff line number Diff line
@@ -7616,7 +7616,7 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById, UsesCreateAndUpd 
        order_by=lambda: -Workflow.id,

        cascade_backrefs=False,

    )

    latest_workflow = relationship(

    latest_workflow: Mapped["Workflow"] = relationship(

        "Workflow",

        post_update=True,

        primaryjoin=(lambda: StoredWorkflow.latest_workflow_id == Workflow.id),
@@ -7722,7 +7722,7 @@ class StoredWorkflow(Base, HasTags, Dictifiable, RepresentById, UsesCreateAndUpd 
        )

        return bool(sa_session.scalar(stmt))



    def copy_tags_from(self, target_user, source_workflow):

    def copy_tags_from(self, target_user, source_workflow: "StoredWorkflow"):

        # Override to only copy owner tags.

        for src_swta in source_workflow.owner_tags:

            new_swta = src_swta.copy()
@@ -7895,7 +7895,7 @@ class Workflow(Base, Dictifiable, RepresentById): 
        """

        return self.top_level_workflow.stored_workflow



    def copy(self, user=None):

    def copy(self, user: User):

        """Copy a workflow for a new StoredWorkflow object.



        Pass user if user-specific information needed.
@@ -8206,7 +8206,7 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime): 
                break

        return target_output



    def copy_to(self, copied_step, step_mapping, user=None):

    def copy_to(self, copied_step: "WorkflowStep", step_mapping: Dict[int, "WorkflowStep"], user: User):

        copied_step.order_index = self.order_index

        copied_step.type = self.type

        copied_step.tool_id = self.tool_id
@@ -8238,10 +8238,10 @@ class WorkflowStep(Base, RepresentById, UsesCreateAndUpdateTime): 
                copied_step.subworkflow = subworkflow

                copied_subworkflow = subworkflow

            else:

                # Can this even happen, building a workflow with a subworkflow you don't own ?

                copied_subworkflow = subworkflow.copy()

                # Importing a shared workflow with a subworkflow step

                copied_subworkflow = subworkflow.copy(user=user)

                stored_workflow = StoredWorkflow(

                    user, name=copied_subworkflow.name, workflow=copied_subworkflow, hidden=True

                    user=user, name=copied_subworkflow.name, workflow=copied_subworkflow, hidden=True

                )

                copied_subworkflow.stored_workflow = stored_workflow

                copied_step.subworkflow = copied_subworkflow

lib/galaxy/webapps/base/controller.py

+1 −1
Original line number Diff line number Diff line
@@ -1144,7 +1144,7 @@ class UsesStoredWorkflowMixin(SharableItemSecurityMixin, UsesAnnotations): 
            except exceptions.ToolMissingException:

                pass



    def _import_shared_workflow(self, trans, stored):

    def _import_shared_workflow(self, trans, stored: model.StoredWorkflow):

        """Imports a shared workflow"""

        # Copy workflow.

        imported_stored = model.StoredWorkflow()