fix: empty store bugs (#592)

Co-authored-by: Marcus Schiesser <mail@marcusschiesser.de>

.changeset/healthy-penguins-pretend.md

+---
+"llamaindex": patch
+---
+
+fixed removeRefDocNode and persist store on delete

packages/core/src/storage/docStore/KVDocumentStore.ts

-import _, * as lodash from "lodash";
+import _ from "lodash";
 import type { BaseNode } from "../../Node.js";
 import { ObjectType } from "../../Node.js";
 import { DEFAULT_NAMESPACE } from "../constants.js";
@@ -123,10 +123,10 @@ export class KVDocumentStore extends BaseDocumentStore {
 
     const refDocInfo = await this.kvstore.get(refDocId, this.refDocCollection);
     if (!_.isNil(refDocInfo)) {
-      lodash.pull(refDocInfo.docIds, docId);
+      !_.pull(refDocInfo.nodeIds, docId);
 
-      if (refDocInfo.docIds.length > 0) {
-        this.kvstore.put(refDocId, refDocInfo.toDict(), this.refDocCollection);
+      if (refDocInfo.nodeIds.length > 0) {
+        this.kvstore.put(refDocId, refDocInfo, this.refDocCollection);
       }
       this.kvstore.delete(refDocId, this.metadataCollection);
     }

packages/core/src/storage/kvStore/SimpleKVStore.ts

@@ -54,6 +54,9 @@ export class SimpleKVStore extends BaseKVStore {
   ): Promise<boolean> {
     if (key in this.data[collection]) {
       delete this.data[collection][key];
+      if (this.persistPath) {
+        await this.persist(this.persistPath, this.fs);
+      }
       return true;
     }
     return false;

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

@@ -82,6 +82,9 @@ export class SimpleVectorStore implements VectorStore {
       delete this.data.embeddingDict[textId];
       delete this.data.textIdToRefDocId[textId];
     }
+    if (this.persistPath) {
+      await this.persist(this.persistPath, this.fs);
+    }
     return Promise.resolve();
   }