Cleanup updating stored_workflow attributes in workflows manager.

The ever careless @jmchilton did the same thing in two slightly different ways between galaxyproject#10988 and galaxyproject#11001 - creating his own bizarre race condition.
jmchilton · Dec 30, 2020 · a45cdbd · a45cdbd
1 parent c2b1b87
commit a45cdbd
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Showing 3 changed files with 3 additions and 10 deletions.
diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
@@ -413,18 +413,11 @@ def update_workflow_from_raw_description(self, trans, stored_workflow, raw_workf
                 errors.append("Step %i: Requires tool '%s'." % (int(missing_tool_tup[3]) + 1, missing_tool_tup[0]))
             raise MissingToolsException(workflow, errors)
 
-        as_dict = raw_workflow_description.as_dict
-        if 'name' in as_dict:
-            sanitized_name = sanitize_html(as_dict['name'])
-            workflow.name = sanitized_name
-            stored_workflow.name = sanitized_name
-
         # 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):
+        if kwds.get("update_stored_workflow_attributes", True):
             update_dict = raw_workflow_description.as_dict
             if 'name' in update_dict:
                 stored_workflow.name = update_dict['name']
@@ -1425,7 +1418,6 @@ def refactor(self, trans, stored_workflow, refactor_request):
                 stored_workflow,
                 raw_workflow_description,
                 fill_defaults=True,
-                update_stored_workflow_attributes=True,
             )
 
 

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -598,7 +598,7 @@ def update(self, trans, id, payload, **kwds):
                 stored_workflow.published = workflow_dict['published']
                 trans.sa_session.flush()
 
-            if 'annotation' in workflow_dict:
+            if 'annotation' in workflow_dict and not steps_updated:
                 newAnnotation = sanitize_html(workflow_dict['annotation'])
                 self.add_item_annotation(trans.sa_session, trans.get_user(), stored_workflow, newAnnotation)
                 trans.sa_session.flush()

diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -609,6 +609,7 @@ def save_workflow_as(self, trans, workflow_name, workflow_data, workflow_annotat
                     stored_workflow,
                     workflow_data,
                     from_tool_form=from_tool_form,
+                    update_stored_workflow_attributes=False,  # taken care of above
                 )
             except workflows.MissingToolsException as e:
                 return dict(