import asyncio
import html
import os
from dataclasses import dataclass
from typing import Any, Union, cast
import networkx as nx
import numpy as np
from nano_vectordb import NanoVectorDB
from .utils import (
logger,
load_json,
write_json,
compute_mdhash_id,
)
from .base import (
BaseGraphStorage,
BaseKVStorage,
BaseVectorStorage,
)
@dataclass
class JsonKVStorage(BaseKVStorage):
def __post_init__(self):
working_dir = self.global_config["working_dir"]
self._file_name = os.path.join(working_dir, f"kv_store_{self.namespace}.json")
self._data = load_json(self._file_name) or {}
logger.info(f"Load KV {self.namespace} with {len(self._data)} data")
async def all_keys(self) -> list[str]:
return list(self._data.keys())
async def index_done_callback(self):
write_json(self._data, self._file_name)
async def get_by_id(self, id):
return self._data.get(id, None)
async def get_by_ids(self, ids, fields=None):
if fields is None:
return [self._data.get(id, None) for id in ids]
return [
(
{k: v for k, v in self._data[id].items() if k in fields}
if self._data.get(id, None)
else None
)
for id in ids
]
async def filter_keys(self, data: list[str]) -> set[str]:
return set([s for s in data if s not in self._data])
async def upsert(self, data: dict[str, dict]):
left_data = {k: v for k, v in data.items() if k not in self._data}
self._data.update(left_data)
return left_data
async def drop(self):
self._data = {}
@dataclass
class NanoVectorDBStorage(BaseVectorStorage):
cosine_better_than_threshold: float = 0.2
def __post_init__(self):
self._client_file_name = os.path.join(
self.global_config["working_dir"], f"vdb_{self.namespace}.json"
)
self._max_batch_size = self.global_config["embedding_batch_num"]
self._client = NanoVectorDB(
self.embedding_func.embedding_dim, storage_file=self._client_file_name
)
self.cosine_better_than_threshold = self.global_config.get(
"cosine_better_than_threshold", self.cosine_better_than_threshold
)
async def upsert(self, data: dict[str, dict]):
logger.info(f"Inserting {len(data)} vectors to {self.namespace}")
if not len(data):
logger.warning("You insert an empty data to vector DB")
return []
list_data = [
{
"__id__": k,
**{k1: v1 for k1, v1 in v.items() if k1 in self.meta_fields},
}
for k, v in data.items()
]
contents = [v["content"] for v in data.values()]
batches = [
contents[i : i + self._max_batch_size]
for i in range(0, len(contents), self._max_batch_size)
]
embeddings_list = await asyncio.gather(
*[self.embedding_func(batch) for batch in batches]
)
embeddings = np.concatenate(embeddings_list)
for i, d in enumerate(list_data):
d["__vector__"] = embeddings[i]
results = self._client.upsert(datas=list_data)
return results
async def query(self, query: str, top_k=5):
embedding = await self.embedding_func([query])
embedding = embedding[0]
results = self._client.query(
query=embedding,
top_k=top_k,
better_than_threshold=self.cosine_better_than_threshold,
)
results = [
{**dp, "id": dp["__id__"], "distance": dp["__metrics__"]} for dp in results
]
return results
@property
def client_storage(self):
return getattr(self._client, "_NanoVectorDB__storage")
async def delete_entity(self, entity_name: str):
try:
entity_id = [compute_mdhash_id(entity_name, prefix="ent-")]
if self._client.get(entity_id):
self._client.delete(entity_id)
logger.info(f"Entity {entity_name} have been deleted.")
else:
logger.info(f"No entity found with name {entity_name}.")
except Exception as e:
logger.error(f"Error while deleting entity {entity_name}: {e}")
async def delete_relation(self, entity_name: str):
try:
relations = [
dp
for dp in self.client_storage["data"]
if dp["src_id"] == entity_name or dp["tgt_id"] == entity_name
]
ids_to_delete = [relation["__id__"] for relation in relations]
if ids_to_delete:
self._client.delete(ids_to_delete)
logger.info(
f"All relations related to entity {entity_name} have been deleted."
)
else:
logger.info(f"No relations found for entity {entity_name}.")
except Exception as e:
logger.error(
f"Error while deleting relations for entity {entity_name}: {e}"
)
async def index_done_callback(self):
self._client.save()
@dataclass
class NetworkXStorage(BaseGraphStorage):
@staticmethod
def load_nx_graph(file_name) -> nx.Graph:
if os.path.exists(file_name):
return nx.read_graphml(file_name)
return None
@staticmethod
def write_nx_graph(graph: nx.Graph, file_name):
logger.info(
f"Writing graph with {graph.number_of_nodes()} nodes, {graph.number_of_edges()} edges"
)
nx.write_graphml(graph, file_name)
@staticmethod
def stable_largest_connected_component(graph: nx.Graph) -> nx.Graph:
"""Refer to https://github.com/microsoft/graphrag/index/graph/utils/stable_lcc.py
Return the largest connected component of the graph, with nodes and edges sorted in a stable way.
"""
from graspologic.utils import largest_connected_component
graph = graph.copy()
graph = cast(nx.Graph, largest_connected_component(graph))
node_mapping = {
node: html.unescape(node.upper().strip()) for node in graph.nodes()
} # type: ignore
graph = nx.relabel_nodes(graph, node_mapping)
return NetworkXStorage._stabilize_graph(graph)
@staticmethod
def _stabilize_graph(graph: nx.Graph) -> nx.Graph:
"""Refer to https://github.com/microsoft/graphrag/index/graph/utils/stable_lcc.py
Ensure an undirected graph with the same relationships will always be read the same way.
"""
fixed_graph = nx.DiGraph() if graph.is_directed() else nx.Graph()
sorted_nodes = graph.nodes(data=True)
sorted_nodes = sorted(sorted_nodes, key=lambda x: x[0])
fixed_graph.add_nodes_from(sorted_nodes)
edges = list(graph.edges(data=True))
if not graph.is_directed():
def _sort_source_target(edge):
source, target, edge_data = edge
if source > target:
temp = source
source = target
target = temp
return source, target, edge_data
edges = [_sort_source_target(edge) for edge in edges]
def _get_edge_key(source: Any, target: Any) -> str:
return f"{source} -> {target}"
edges = sorted(edges, key=lambda x: _get_edge_key(x[0], x[1]))
fixed_graph.add_edges_from(edges)
return fixed_graph
def __post_init__(self):
self._graphml_xml_file = os.path.join(
self.global_config["working_dir"], f"graph_{self.namespace}.graphml"
)
preloaded_graph = NetworkXStorage.load_nx_graph(self._graphml_xml_file)
if preloaded_graph is not None:
logger.info(
f"Loaded graph from {self._graphml_xml_file} with {preloaded_graph.number_of_nodes()} nodes, {preloaded_graph.number_of_edges()} edges"
)
self._graph = preloaded_graph or nx.Graph()
self._node_embed_algorithms = {
"node2vec": self._node2vec_embed,
}
async def index_done_callback(self):
NetworkXStorage.write_nx_graph(self._graph, self._graphml_xml_file)
async def has_node(self, node_id: str) -> bool:
return self._graph.has_node(node_id)
async def has_edge(self, source_node_id: str, target_node_id: str) -> bool:
return self._graph.has_edge(source_node_id, target_node_id)
async def get_node(self, node_id: str) -> Union[dict, None]:
return self._graph.nodes.get(node_id)
async def node_degree(self, node_id: str) -> int:
return self._graph.degree(node_id)
async def edge_degree(self, src_id: str, tgt_id: str) -> int:
return self._graph.degree(src_id) + self._graph.degree(tgt_id)
async def get_edge(
self, source_node_id: str, target_node_id: str
) -> Union[dict, None]:
return self._graph.edges.get((source_node_id, target_node_id))
async def get_node_edges(self, source_node_id: str):
if self._graph.has_node(source_node_id):
return list(self._graph.edges(source_node_id))
return None
async def upsert_node(self, node_id: str, node_data: dict[str, str]):
self._graph.add_node(node_id, **node_data)
async def upsert_edge(
self, source_node_id: str, target_node_id: str, edge_data: dict[str, str]
):
self._graph.add_edge(source_node_id, target_node_id, **edge_data)
async def delete_node(self, node_id: str):
"""
Delete a node from the graph based on the specified node_id.
:param node_id: The node_id to delete
"""
if self._graph.has_node(node_id):
self._graph.remove_node(node_id)
logger.info(f"Node {node_id} deleted from the graph.")
else:
logger.warning(f"Node {node_id} not found in the graph for deletion.")
async def embed_nodes(self, algorithm: str) -> tuple[np.ndarray, list[str]]:
if algorithm not in self._node_embed_algorithms:
raise ValueError(f"Node embedding algorithm {algorithm} not supported")
return await self._node_embed_algorithms[algorithm]()
# @TODO: NOT USED
async def _node2vec_embed(self):
from graspologic import embed
embeddings, nodes = embed.node2vec_embed(
self._graph,
**self.global_config["node2vec_params"],
)
nodes_ids = [self._graph.nodes[node_id]["id"] for node_id in nodes]
return embeddings, nodes_ids