refactor: encapsulate node serialization

packages/core/src/Node.ts

+import _ from "lodash";
 import { createHash } from "node:crypto";
 import path from "path";
 import { v4 as uuidv4 } from "uuid";
@@ -141,12 +142,26 @@ export abstract class BaseNode<T extends Metadata = Metadata> {
   }
 
   /**
-   * Used with built in JSON.stringify
-   * @returns
+   * Called by built in JSON.stringify (see https://javascript.info/json)
+   * Properties are read-only as they are not deep-cloned (not necessary for stringification).
+   * @see toMutableJSON - use to return a mutable JSON instead
    */
   toJSON(): Record<string, any> {
     return { ...this, type: this.getType() };
   }
+
+  clone(): BaseNode {
+    return jsonToNode(this.toMutableJSON()) as BaseNode;
+  }
+
+  /**
+   * Converts the object to a JSON representation.
+   * Properties can be safely modified as a deep clone of the properties are created.
+   * @return {Record<string, any>} - The JSON representation of the object.
+   */
+  toMutableJSON(): Record<string, any> {
+    return _.cloneDeep(this.toJSON());
+  }
 }
 
 /**

packages/core/src/indices/vectorStore/VectorStoreIndex.ts

@@ -4,7 +4,6 @@ import {
   ImageNode,
   MetadataMode,
   ObjectType,
-  jsonToNode,
   splitNodesByType,
 } from "../../Node";
 import { BaseQueryEngine, RetrieverQueryEngine } from "../../QueryEngine";
@@ -278,7 +277,7 @@ export class VectorStoreIndex extends BaseIndex<IndexDict> {
         type === ObjectType.INDEX ||
         type === ObjectType.IMAGE
       ) {
-        const nodeWithoutEmbedding = jsonToNode(nodes[i].toJSON());
+        const nodeWithoutEmbedding = nodes[i].clone();
         nodeWithoutEmbedding.embedding = undefined;
         this.indexStruct.addNode(nodeWithoutEmbedding, newIds[i]);
         this.docStore.addDocuments([nodeWithoutEmbedding], true);

packages/core/src/storage/vectorStore/utils.ts

-import _ from "lodash";
 import { BaseNode, jsonToNode, Metadata, ObjectType } from "../../Node";
 
 const DEFAULT_TEXT_KEY = "text";
@@ -17,7 +16,7 @@ export function nodeToMetadata(
   textField: string = DEFAULT_TEXT_KEY,
   flatMetadata: boolean = false,
 ): Metadata {
-  const { metadata, embedding, ...rest } = _.cloneDeep(node.toJSON());
+  const { metadata, embedding, ...rest } = node.toMutableJSON();
 
   if (flatMetadata) {
     validateIsFlat(metadata);