Merge remote-tracking branch 'upstream/release_19.05' into dev

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

@@ -552,7 +552,8 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
                     if (trans.security.decode_id(id) in entries):
                         trans.get_user().stored_workflow_menu_entries.remove(entries[trans.security.decode_id(id)])
             # set tags
-            trans.app.tag_handler.set_tags_from_list(user=trans.user, item=stored_workflow, new_tags_list=workflow_dict.get('tags', []))
+            if 'tags' in workflow_dict:
+                trans.app.tag_handler.set_tags_from_list(user=trans.user, item=stored_workflow, new_tags_list=workflow_dict['tags'])
 
             if 'steps' in workflow_dict:
                 try:
@@ -565,9 +566,6 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
                     )
                 except workflows.MissingToolsException:
                     raise exceptions.MessageException("This workflow contains missing tools. It cannot be saved until they have been removed from the workflow or installed.")
-            else:
-                # We only adjusted tags and menu entry
-                return payload
         else:
             message = "Updating workflow requires dictionary containing 'workflow' attribute with new JSON description."
             raise exceptions.RequestParameterInvalidException(message)

lib/galaxy/workflow/modules.py

@@ -594,7 +594,7 @@ class InputModule(WorkflowModule):
         progress.set_outputs_for_input(invocation_step, step_outputs)
 
     def recover_mapping(self, invocation_step, progress):
-        progress.set_outputs_for_input(invocation_step)
+        progress.set_outputs_for_input(invocation_step, already_persisted=True)
 
 
 class InputDataModule(InputModule):
@@ -1305,17 +1305,6 @@ class ToolModule(WorkflowModule):
 
         return complete
 
-    def recover_mapping(self, invocation_step, progress):
-        outputs = {}
-
-        for output_dataset_assoc in invocation_step.output_datasets:
-            outputs[output_dataset_assoc.output_name] = output_dataset_assoc.dataset
-
-        for output_dataset_collection_assoc in invocation_step.output_dataset_collections:
-            outputs[output_dataset_collection_assoc.output_name] = output_dataset_collection_assoc.dataset_collection
-
-        progress.set_step_outputs(invocation_step, outputs)
-
     def _effective_post_job_actions(self, step):
         effective_post_job_actions = step.post_job_actions[:]
         for key, value in self.runtime_post_job_actions.items():

lib/galaxy/workflow/run.py

@@ -405,7 +405,7 @@ class WorkflowProgress(object):
         else:
             return step_outputs[output_name]
 
-    def set_outputs_for_input(self, invocation_step, outputs=None):
+    def set_outputs_for_input(self, invocation_step, outputs=None, already_persisted=False):
         step = invocation_step.workflow_step
 
         if outputs is None:
@@ -420,7 +420,7 @@ class WorkflowProgress(object):
             elif step_id in self.inputs_by_step_id:
                 outputs['output'] = self.inputs_by_step_id[step_id]
 
-        self.set_step_outputs(invocation_step, outputs)
+        self.set_step_outputs(invocation_step, outputs, already_persisted=already_persisted)
 
     def set_step_outputs(self, invocation_step, outputs, already_persisted=False):
         step = invocation_step.workflow_step

test/api/test_workflows.py

@@ -343,6 +343,20 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase):
         # Make sure the positions have been updated.
         map(tweak_step, updated_workflow_content['steps'].items())
 
+    def test_update_tags(self):
+        workflow_object = self.workflow_populator.load_workflow(name="test_import")
+        upload_response = self.__test_upload(workflow=workflow_object)
+        workflow = upload_response.json()
+        workflow['tags'] = ['a_tag', 'b_tag']
+        update_response = self._update_workflow(workflow['id'], workflow).json()
+        assert update_response['tags'] == ['a_tag', 'b_tag']
+        del workflow['tags']
+        update_response = self._update_workflow(workflow['id'], workflow).json()
+        assert update_response['tags'] == ['a_tag', 'b_tag']
+        workflow['tags'] = []
+        update_response = self._update_workflow(workflow['id'], workflow).json()
+        assert update_response['tags'] == []
+
     def test_update_no_tool_id(self):
         workflow_object = self.workflow_populator.load_workflow(name="test_import")
         upload_response = self.__test_upload(workflow=workflow_object)