Rework refactoring API for better separation of concerns.

Thinner controller, pydantic model to separate options available for manager (which has to render a response) from those of the refactoring executor.

lib/galaxy/managers/workflows.py

@@ -45,6 +45,7 @@ from galaxy.workflow.modules import (
     WorkflowModuleInjector
 )
 from galaxy.workflow.refactor.execute import WorkflowRefactorExecutor
+from galaxy.workflow.refactor.schema import RefactorActions
 from galaxy.workflow.reports import generate_report
 from galaxy.workflow.resources import get_resource_mapper_function
 from galaxy.workflow.steps import attach_ordered_steps
@@ -1408,7 +1409,7 @@ class WorkflowContentsManager(UsesAnnotations):
             if default_label and util.unicodify(default_label).lower() not in ['input dataset', 'input dataset collection']:
                 step.label = module.label = default_label
 
-    def refactor(self, trans, stored_workflow, refactor_request):
+    def do_refactor(self, trans, stored_workflow, refactor_request):
         """Apply supplied actions to stored_workflow.latest_workflow to build a new version.
         """
         workflow = stored_workflow.latest_workflow
@@ -1434,6 +1435,15 @@ class WorkflowContentsManager(UsesAnnotations):
                 workflow_update_options,
             )
 
+    def refactor(self, trans, stored_workflow, refactor_request):
+        stored_workflow, errors = self.do_refactor(trans, stored_workflow, refactor_request)
+        # TODO: handle errors...
+        return self.workflow_to_dict(trans, stored_workflow, style=refactor_request.style)
+
+
+class RefactorRequest(RefactorActions):
+    style: str = "export"
+
 
 class WorkflowStateResolutionOptions(BaseModel):
     # fill in default tool state when updating, may change tool_state

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -24,6 +24,7 @@ from galaxy.managers import (
 from galaxy.managers.jobs import fetch_job_states, invocation_job_source_iter, summarize_job_metrics
 from galaxy.managers.workflows import (
     MissingToolsException,
+    RefactorRequest,
     WorkflowCreateOptions,
     WorkflowUpdateOptions,
 )
@@ -49,7 +50,6 @@ from galaxy.webapps.base.controller import (
 )
 from galaxy.workflow.extract import extract_workflow
 from galaxy.workflow.modules import module_factory
-from galaxy.workflow.refactor.schema import RefactorRequest
 from galaxy.workflow.run import invoke, queue_invoke
 from galaxy.workflow.run_request import build_workflow_run_configs
 
@@ -656,12 +656,9 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         """
         stored_workflow = self.__get_stored_workflow(trans, id, **kwds)
         refactor_request = RefactorRequest(**payload)
-        style = payload.get("style", "export")
-        result, errors = self.workflow_contents_manager.refactor(
+        return self.workflow_contents_manager.refactor(
             trans, stored_workflow, refactor_request
         )
-        # TODO: handle errors...
-        return self.workflow_contents_manager.workflow_to_dict(trans, stored_workflow, style=style)
 
     @expose_api
     def build_module(self, trans, payload=None):

lib/galaxy/workflow/refactor/execute.py

@@ -22,7 +22,7 @@ from .schema import (
     FillStepDefaultsAction,
     InputReferenceByOrderIndex,
     OutputReferenceByOrderIndex,
-    RefactorRequest,
+    RefactorActions,
     RemoveUnlabeledWorkflowOutputs,
     step_reference_union,
     StepReferenceByLabel,
@@ -51,7 +51,7 @@ class WorkflowRefactorExecutor:
         self.workflow = workflow
         self.module_injector = module_injector
 
-    def refactor(self, refactor_request: RefactorRequest):
+    def refactor(self, refactor_request: RefactorActions):
         for action in refactor_request.actions:
             action_type = action.action_type
             refactor_method_name = "_apply_%s" % action_type

lib/galaxy/workflow/refactor/schema.py

@@ -196,6 +196,6 @@ for action_class in union_action_classes.__args__:  # type: ignore
     ACTION_CLASSES_BY_TYPE[action_type] = action_class
 
 
-class RefactorRequest(BaseModel):
+class RefactorActions(BaseModel):
     actions: List[Action]
     dry_run: bool = False

test/integration/test_workflow_refactoring.py

@@ -1,7 +1,7 @@
 import json
 
 from galaxy.managers.context import ProvidesAppContext
-from galaxy.workflow.refactor.schema import RefactorRequest
+from galaxy.workflow.refactor.schema import RefactorActions
 from galaxy_test.base.populators import (
     WorkflowPopulator,
 )
@@ -320,10 +320,10 @@ steps:
     def _refactor(self, actions):
         user = self._app.model.session.query(self._app.model.User).order_by(self._app.model.User.id.desc()).limit(1).one()
         mock_trans = MockTrans(self._app, user)
-        return self._manager.refactor(
+        return self._manager.do_refactor(
             mock_trans,
             self._most_recent_stored_workflow,
-            RefactorRequest(**{"actions": actions})
+            RefactorActions(**{"actions": actions})
         )
 
     @property

test/unit/workflows/test_refactor_models.py

@@ -1,4 +1,4 @@
-from galaxy.workflow.refactor.schema import RefactorRequest
+from galaxy.workflow.refactor.schema import RefactorActions
 
 
 def test_root_list():
@@ -16,7 +16,7 @@ def test_root_list():
             {"action_type": "extract_legacy_parameter", "name": "foo", "label": "new_foo"},
         ],
     }
-    ar = RefactorRequest(**request)
+    ar = RefactorActions(**request)
     actions = ar.actions
 
     a0 = actions[0]