API for structured workflow refactoring.

lib/galaxy/app.py

@@ -20,7 +20,7 @@
 from galaxy.managers.roles import RoleManager
 from galaxy.managers.tools import DynamicToolManager
 from galaxy.managers.users import UserManager
-from galaxy.managers.workflows import WorkflowsManager
+from galaxy.managers.workflows import WorkflowContentsManager, WorkflowsManager
 from galaxy.model.database_heartbeat import DatabaseHeartbeat
 from galaxy.model.tags import GalaxyTagHandler
 from galaxy.queue_worker import (
@@ -105,6 +105,7 @@ def __init__(self, **kwargs):
         self.history_manager = HistoryManager(self)
         self.hda_manager = HDAManager(self)
         self.workflow_manager = WorkflowsManager(self)
+        self.workflow_contents_manager = WorkflowContentsManager(self)
         self.dependency_resolvers_view = DependencyResolversView(self)
         self.test_data_resolver = test_data.TestDataResolver(file_dirs=self.config.tool_test_data_directories)
         self.library_folder_manager = FolderManager()

lib/galaxy/managers/workflows.py

@@ -39,6 +39,7 @@
     ToolModule,
     WorkflowModuleInjector
 )
+from galaxy.workflow.refactor.execute import WorkflowRefactorExecutor
 from galaxy.workflow.reports import generate_report
 from galaxy.workflow.resources import get_resource_mapper_function
 from galaxy.workflow.steps import attach_ordered_steps
@@ -305,7 +306,7 @@ def normalize_workflow_format(self, trans, as_dict):
 
         Currently this mostly means converting format 2 workflows into standard Galaxy
         workflow JSON for consumption for the rest of this module. In the future we will
-        want to be a lot more percise about this - preserve the original description along
+        want to be a lot more precise about this - preserve the original description along
         side the data model and apply updates in a way that largely preserves YAML structure
         so workflows can be extracted.
         """
@@ -415,6 +416,16 @@ def update_workflow_from_raw_description(self, trans, stored_workflow, raw_workf
         # Connect up
         workflow.stored_workflow = stored_workflow
         stored_workflow.latest_workflow = workflow
+
+        # I'm not sure we can't just default this to True.
+        if kwds.get("update_stored_workflow_attributes", False):
+            update_dict = raw_workflow_description.as_dict
+            if 'name' in update_dict:
+                stored_workflow.name = update_dict['name']
+            if 'annotation' in update_dict:
+                newAnnotation = sanitize_html(update_dict['annotation'])
+                self.add_item_annotation(trans.sa_session, stored_workflow.user, stored_workflow, newAnnotation)
+
         # Persist
         trans.sa_session.flush()
         if stored_workflow.from_path:
@@ -439,6 +450,12 @@ def _workflow_from_raw_description(self, trans, raw_workflow_description, name,
         if 'report' in data:
             workflow.reports_config = data['report']
 
+        if 'license' in data:
+            workflow.license = data['license']
+
+        if 'creator' in data:
+            workflow.creator_metadata = data['creator']
+
         # Assume no errors until we find a step that has some
         workflow.has_errors = False
         # Create each step
@@ -520,7 +537,7 @@ def to_format_2(wf_dict, **kwds):
         elif style == "ga":
             wf_dict = self._workflow_to_dict_export(trans, stored, workflow=workflow)
         else:
-            raise exceptions.RequestParameterInvalidException('Unknown workflow style [%s]' % style)
+            raise exceptions.RequestParameterInvalidException(f'Unknown workflow style {style}')
         if version is not None:
             wf_dict['version'] = version
         else:
@@ -735,7 +752,6 @@ def _workflow_to_dict_editor(self, trans, stored, workflow, tooltip=True, is_sub
         data['upgrade_messages'] = {}
         data['report'] = workflow.reports_config or {}
         data['license'] = workflow.license
-        log.info("creator_metadata is %s" % workflow.creator_metadata)
         data['creator'] = workflow.creator_metadata
 
         output_label_index = set()
@@ -1254,8 +1270,7 @@ def __module_from_dict(self, trans, steps, steps_by_external_id, step_dict, **kw
         representing type-specific functionality from the incoming dictionary.
         """
         step = model.WorkflowStep()
-        # TODO: Consider handling position inside module.
-        step.position = step_dict['position']
+        step.position = step_dict.get('position', model.WorkflowStep.DEFAULT_POSITION)
         if step_dict.get("uuid", None) and step_dict['uuid'] != "None":
             step.uuid = step_dict["uuid"]
         if "label" in step_dict:
@@ -1265,13 +1280,13 @@ def __module_from_dict(self, trans, steps, steps_by_external_id, step_dict, **kw
         self.__set_default_label(step, module, step_dict.get('tool_state'))
         module.save_to_step(step)
 
-        annotation = step_dict['annotation']
+        annotation = step_dict.get('annotation')
         if annotation:
             annotation = sanitize_html(annotation)
             self.add_item_annotation(trans.sa_session, trans.get_user(), step, annotation)
 
         # Stick this in the step temporarily
-        step.temp_input_connections = step_dict['input_connections']
+        step.temp_input_connections = step_dict.get('input_connections', {})
 
         # Create the model class for the step
         steps.append(step)
@@ -1380,6 +1395,28 @@ def __set_default_label(self, step, module, state):
             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):
+        """Apply supplied actions to stored_workflow.latest_workflow to build a new version.
+        """
+        workflow = stored_workflow.latest_workflow
+        as_dict = self.workflow_to_dict(trans, stored_workflow, style="ga")
+        raw_workflow_description = self.normalize_workflow_format(trans, as_dict)
+        module_injector = WorkflowModuleInjector(trans)
+        WorkflowRefactorExecutor(raw_workflow_description, workflow, module_injector).refactor(refactor_request)
+        if refactor_request.dry_run:
+            # TODO: go a bit further with dry run, try to re-populate a workflow just
+            # don't flush it or tie it to the stored_workflow. Still for now, there is
+            # a lot of things that would be caught with just what is done here.
+            return None, []
+        else:
+            return self.update_workflow_from_raw_description(
+                trans,
+                stored_workflow,
+                raw_workflow_description,
+                fill_defaults=True,
+                update_stored_workflow_attributes=True,
+            )
+
 
 class MissingToolsException(exceptions.MessageException):
 

lib/galaxy/model/__init__.py

@@ -4894,6 +4894,12 @@ def step_by_index(self, order_index):
                 return step
         raise KeyError("Workflow has no step with order_index '%s'" % order_index)
 
+    def step_by_label(self, label):
+        for step in self.steps:
+            if label == step.label:
+                return step
+        raise KeyError("Workflow has no step with label '%s'" % label)
+
     @property
     def input_steps(self):
         for step in self.steps:
@@ -4983,6 +4989,7 @@ class WorkflowStep(RepresentById):
         "data_collection_input": "dataset_collection",
         "parameter_input": "parameter",
     }
+    DEFAULT_POSITION = {"left": 0, "top": 0}
 
     def __init__(self):
         self.id = None

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

@@ -45,6 +45,7 @@
 )
 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
 
@@ -646,6 +647,31 @@ def update(self, trans, id, payload, **kwds):
             raise exceptions.RequestParameterInvalidException(message)
         return self.workflow_contents_manager.workflow_to_dict(trans, stored_workflow, style="instance")
 
+    @expose_api
+    def refactor(self, trans, id, payload, **kwds):
+        """
+        * PUT /api/workflows/{id}/refactor
+            updates the workflow stored with ``id``
+
+        :type   id:      str
+        :param  id:      the encoded id of the workflow to update
+        :param  instance:                 true if fetch by Workflow ID instead of StoredWorkflow id, false
+                                          by default.
+        :type   instance:                 boolean
+        :type   payload: dict
+        :param  payload: a dictionary containing list of actions to apply.
+        :rtype:     dict
+        :returns:   serialized version of the workflow
+        """
+        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(
+            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/webapps/galaxy/buildapp.py

@@ -445,6 +445,7 @@ def populate_api_routes(webapp, app):
     webapp.mapper.connect('/api/workflows/build_module', action='build_module', controller="workflows")
     webapp.mapper.connect('/api/workflows/menu', action='get_workflow_menu', controller="workflows", conditions=dict(method=["GET"]))
     webapp.mapper.connect('/api/workflows/menu', action='set_workflow_menu', controller="workflows", conditions=dict(method=["PUT"]))
+    webapp.mapper.connect('/api/workflows/{id}/refactor', action='refactor', controller="workflows", conditions=dict(method=["PUT"]))
     webapp.mapper.resource('workflow', 'workflows', path_prefix='/api')
     webapp.mapper.connect('/api/licenses', controller='licenses', action='index')
     webapp.mapper.connect('/api/licenses/{id}', controller='licenses', action='get')

lib/galaxy/workflow/modules.py

@@ -776,6 +776,7 @@ def _parse_state_into_dict(self):
 
 
 class InputParameterModule(WorkflowModule):
+    POSSIBLE_PARAMETER_TYPES = ["text", "integer", "float", "boolean", "color"]
     type = "parameter_input"
     name = "Input parameter"
     default_parameter_type = "text"