diff --git a/graphrag/entity_resolution.py b/graphrag/entity_resolution.py
index 67d351a73..a5be7226c 100644
--- a/graphrag/entity_resolution.py
+++ b/graphrag/entity_resolution.py
@@ -111,7 +111,7 @@ class EntityResolution(Extractor):
         connect_graph.add_edges_from(resolution_result)
         async with trio.open_nursery() as nursery:
             for sub_connect_graph in nx.connected_components(connect_graph):
-                merging_nodes = list(sub_connect_graph.nodes)
+                merging_nodes = list(sub_connect_graph.nodes())
                 nursery.start_soon(lambda: self._merge_graph_nodes(graph, merging_nodes, change))
 
         # Update pagerank
diff --git a/graphrag/general/extractor.py b/graphrag/general/extractor.py
index 4b906903c..d4f9e9946 100644
--- a/graphrag/general/extractor.py
+++ b/graphrag/general/extractor.py
@@ -201,8 +201,7 @@ class Extractor:
             # Merge two nodes, keep "entity_name", "entity_type", "page_rank" unchanged.
             node1_attrs = graph.nodes[node1]
             node0_attrs["description"] += f"{GRAPH_FIELD_SEP}{node1_attrs['description']}"
-            for attr in ["keywords", "source_id"]:
-                node0_attrs[attr] = sorted(set(node0_attrs[attr].extend(node1_attrs[attr])))
+            node0_attrs["source_id"] = sorted(set(node0_attrs["source_id"].extend(node1_attrs.get("source_id", []))))
             for neighbor in graph.neighbors(node1):
                 change.removed_edges.add(get_from_to(node1, neighbor))
                 if neighbor not in nodes_set:
@@ -213,8 +212,8 @@ class Extractor:
                         edge0_attrs = graph.get_edge_data(nodes[0], neighbor)
                         edge0_attrs["weight"] += edge1_attrs["weight"]
                         edge0_attrs["description"] += f"{GRAPH_FIELD_SEP}{edge1_attrs['description']}"
-                        edge0_attrs["keywords"] = list(set(edge0_attrs["keywords"].extend(edge1_attrs["keywords"])))
-                        edge0_attrs["source_id"] = list(set(edge0_attrs["source_id"].extend(edge1_attrs["source_id"])))
+                        for attr in ["keywords", "source_id"]:
+                            edge0_attrs[attr] = sorted(set(edge0_attrs[attr].extend(edge1_attrs.get(attr, []))))
                         edge0_attrs["description"] = await self._handle_entity_relation_summary(f"({nodes[0]}, {neighbor})", edge0_attrs["description"])
                         graph.add_edge(nodes[0], neighbor, **edge0_attrs)
                     else:
diff --git a/graphrag/utils.py b/graphrag/utils.py
index d370d0a25..790638716 100644
--- a/graphrag/utils.py
+++ b/graphrag/utils.py
@@ -439,7 +439,7 @@ async def set_graph(tenant_id: str, kb_id: str, embd_mdl, graph: nx.Graph, chang
     if change.removed_edges:
         async with trio.open_nursery() as nursery:
             for from_node, to_node in change.removed_edges:
-                nursery.start_soon(lambda: settings.docStoreConn.delete({"knowledge_graph_kwd": ["relation"], "from_entity_kwd": from_node, "to_entity_kwd": to_node}, search.index_name(tenant_id), kb_id))
+                 nursery.start_soon(lambda: trio.to_thread.run_sync(lambda: settings.docStoreConn.delete({"knowledge_graph_kwd": ["relation"], "from_entity_kwd": from_node, "to_entity_kwd": to_node}, search.index_name(tenant_id), kb_id)))
     now = trio.current_time()
     if callback:
         callback(msg=f"set_graph removed {len(change.removed_nodes)} nodes and {len(change.removed_edges)} edges from index in {now - start:.2f}s.")