User reported an error with using LlamaIndex integrations in MongoDB

https://github.com/run-llama/llama_index/issues/9546

Detailed steps to reproduce the problem?

Here's the code snippet

documents = SimpleDirectoryReader("kg").load_data()
graph_store = NebulaGraphStore(
space_name=space_name,
edge_types=edge_types,
rel_prop_names=rel_prop_names,
tags=tags,
)
docstore = MongoDocumentStore.from_uri(uri=MONGO_URI)
index_store = MongoIndexStore.from_uri(uri=MONGO_URI)

storage_context = StorageContext.from_defaults(
graph_store=graph_store,
docstore=docstore,
index_store=index_store
)
index = KnowledgeGraphIndex.from_documents(
documents,
max_triplets_per_chunk=10,
storage_context=storage_context,
service_context=service_context,
include_embeddings=True,
)

Stack Trace

Traceback (most recent call last):
File "/home/ssm-user/llama/testnebula.py", line 84, in <module>
index = KnowledgeGraphIndex.from_documents(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ssm-user/llama/lib/python3.11/site-packages/llama_index/indices/base.py", line 106, in from_documents
return cls(
^^^^
File "/home/ssm-user/llama/lib/python3.11/site-packages/llama_index/indices/knowledge_graph/base.py", line 81, in _init_
super()._init_(
File "/home/ssm-user/llama/lib/python3.11/site-packages/llama_index/indices/base.py", line 73, in _init_
self._storage_context.index_store.add_index_struct(self._index_struct)
File "/home/ssm-user/llama/lib/python3.11/site-packages/llama_index/storage/index_store/keyval_index_store.py", line 38, in add_index_struct
self._kvstore.put(key, data, collection=self._collection)
File "/home/ssm-user/llama/lib/python3.11/site-packages/llama_index/storage/kvstore/mongodb_kvstore.py",line 112, in put
self._db[collection].replace_one(
File "/home/ssm-user/llama/lib/python3.11/site-packages/pymongo/collection.py", line 973, in replace_one
self._update_retryable(
File "/home/ssm-user/llama/lib/python3.11/site-packages/pymongo/collection.py", line 881, in _update_retryable
return self.__database.client._retryable_write(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ssm-user/llama/lib/python3.11/site-packages/pymongo/mongo_client.py", line 1523, in _retryable_write
return self._retry_with_session(retryable, func, s, bulk)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ssm-user/llama/lib/python3.11/site-packages/pymongo/mongo_client.py", line 1421, in _retry_with_session
return self._retry_internal(
^^^^^^^^^^^^^^^^^^^^^
File "/home/ssm-user/llama/lib/python3.11/site-packages/pymongo/_csot.py", line 107, in csot_wrapper
return func(self, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ssm-user/llama/lib/python3.11/site-packages/pymongo/mongo_client.py", line 1462, in _retry_internal
).run()
^^^^^
File "/home/ssm-user/llama/lib/python3.11/site-packages/pymongo/mongo_client.py", line 2315, in run
return self._read() if self._is_read else self._write()
^^^^^^^^^^^^^
File "/home/ssm-user/llama/lib/python3.11/site-packages/pymongo/mongo_client.py", line 2423, in _write
return self._func(self._session, conn, self._retryable) # type: ignore
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ssm-user/llama/lib/python3.11/site-packages/pymongo/collection.py", line 862, in _update
return self._update(
^^^^^^^^^^^^^
File "/home/ssm-user/llama/lib/python3.11/site-packages/pymongo/collection.py", line 816, in _update
result = conn.command(
^^^^^^^^^^^^^
File "/home/ssm-user/llama/lib/python3.11/site-packages/pymongo/helpers.py", line 322, in inner
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/home/ssm-user/llama/lib/python3.11/site-packages/pymongo/pool.py", line 996, in command
self._raise_connection_failure(error)
File "/home/ssm-user/llama/lib/python3.11/site-packages/pymongo/pool.py", line 968, in command
return command(
^^^^^^^^
File "/home/ssm-user/llama/lib/python3.11/site-packages/pymongo/network.py", line 164, in command
message._raise_document_too_large(name, size, max_bson_size + message._COMMAND_OVERHEAD)
File "/home/ssm-user/llama/lib/python3.11/site-packages/pymongo/message.py", line 1182, in _raise_document_too_large
raise DocumentTooLarge(f"

command document too large")
pymongo.errors.DocumentTooLarge: 'update' command document too large

Definition of done: what must be done to consider the task complete?

Describe how MongoDB is set up. Local vs Hosted, version, topology, load balanced, etc.

Atlas

The operating system and version (e.g. Windows 7, OSX 10.8, ...)

Web framework or asynchronous network library used, if any, with version (e.g. Django 1.7, mod_wsgi 4.3.0, gevent 1.0.1, Tornado 4.0.2, ...)

LLamaIndex