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import html
import os
from tqdm.asyncio import tqdm as tqdm_async
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)
]
async def wrapped_task(batch):
result = await self.embedding_func(batch)
pbar.update(1)
return result
embedding_tasks = [wrapped_task(batch) for batch in batches]
pbar = tqdm_async(
total=len(embedding_tasks), desc="Generating embeddings", unit="batch"
)
embeddings_list = await asyncio.gather(*embedding_tasks)
embeddings = np.concatenate(embeddings_list)
if len(embeddings) == len(list_data):
for i, d in enumerate(list_data):
d["__vector__"] = embeddings[i]
results = self._client.upsert(datas=list_data)
return results
else:
# sometimes the embedding is not returned correctly. just log it.
logger.error(
f"embedding is not 1-1 with data, {len(embeddings)} != {len(list_data)}"
)
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.DiGraph:
if os.path.exists(file_name):
graph = nx.read_graphml(file_name)
# Clean the graph by filtering out None values
clean_graph = nx.DiGraph() if graph.is_directed() else nx.Graph()
# Add nodes with filtered data
for node, data in graph.nodes(data=True):
filtered_data = {k: v for k, v in data.items() if v is not None}
clean_graph.add_node(node, **filtered_data)
# Add edges with filtered data
for u, v, data in graph.edges(data=True):
filtered_data = {k: v_val for k, v_val in data.items() if v_val is not None}
clean_graph.add_edge(u, v, **filtered_data)
return clean_graph
return None
# 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.DiGraph, file_name):
logger.info(
f"Writing graph with {graph.number_of_nodes()} nodes, {graph.number_of_edges()} edges"
)
# Create a clean copy of the graph with None values filtered out
clean_graph = nx.DiGraph() if graph.is_directed() else nx.Graph()
# Add nodes with filtered data
for node, data in graph.nodes(data=True):
filtered_data = {k: v for k, v in data.items() if v is not None}
clean_graph.add_node(node, **filtered_data)
# Add edges with filtered data
for u, v, data in graph.edges(data=True):
filtered_data = {k: v_val for k, v_val in data.items() if v_val is not None}
clean_graph.add_edge(u, v, **filtered_data)
nx.write_graphml(clean_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.lower().strip()) for node in graph.nodes()
} # type: ignore
graph = nx.relabel_nodes(graph, node_mapping)
# Clean the graph by filtering out None values before stabilizing
clean_graph = nx.Graph()
# Add nodes with filtered data
for node, data in graph.nodes(data=True):
filtered_data = {k: v for k, v in data.items() if v is not None}
clean_graph.add_node(node, **filtered_data)
# Add edges with filtered data
for u, v, data in graph.edges(data=True):
filtered_data = {k: v_val for k, v_val in data.items() if v_val is not None}
clean_graph.add_edge(u, v, **filtered_data)
return NetworkXStorage._stabilize_graph(clean_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])
# Add nodes with filtered data
for node, data in sorted_nodes:
filtered_data = {k: v for k, v in data.items() if v is not None}
fixed_graph.add_node(node, **filtered_data)
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]))
# Add edges with filtered data
for u, v, data in edges:
filtered_data = {k: v_val for k, v_val in data.items() if v_val is not None}
fixed_graph.add_edge(u, v, **filtered_data)
return fixed_graph
def __post_init__(self):
self._graphml_xml_file = os.path.join(
self.global_config["working_dir"], f"graph_{self.namespace}.graphml"
)
# Persistent embeddings file (store node embeddings on disk under working dir)
self._node_embeddings_file = os.path.join(
self.global_config["working_dir"], f"kg_node_embeddings_{self.namespace}.json"
)
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"
)
# The load_nx_graph method already cleans the graph, so we can use it directly
self._graph = preloaded_graph
else:
self._graph = nx.DiGraph()
self._node_embed_algorithms = {
"node2vec": self._node2vec_embed,
}
# Add cached NetworkX graph instance
self._cached_nx_graph = None
# In-memory cache is kept empty by default; embeddings are persisted on disk
self._node_embeddings_cache = {}
# Add query embeddings cache
self._query_embeddings_cache = {}
def _invalidate_node_embeddings_file(self):
"""Remove persisted embeddings file to avoid stale data."""
try:
if os.path.exists(self._node_embeddings_file):
os.remove(self._node_embeddings_file)
logger.info(
f"Removed stale node embeddings file: {self._node_embeddings_file}"
)
except Exception as e:
logger.warning(
f"Failed to remove node embeddings file {self._node_embeddings_file}: {e}"
)
async def index_done_callback(self):
# Clean the graph before writing to ensure no None values
clean_graph = nx.DiGraph() if self._graph.is_directed() else nx.Graph()
# Add nodes with filtered data
for node, data in self._graph.nodes(data=True):
filtered_data = {k: v for k, v in data.items() if v is not None}
clean_graph.add_node(node, **filtered_data)
# Add edges with filtered data
for u, v, data in self._graph.edges(data=True):
filtered_data = {k: v_val for k, v_val in data.items() if v_val is not None}
clean_graph.add_edge(u, v, **filtered_data)
NetworkXStorage.write_nx_graph(clean_graph, self._graphml_xml_file)
# Clear cache as graph may have been updated
self._cached_nx_graph = None
self._node_embeddings_cache = {}
# Remove persisted node embeddings file to avoid stale embeddings
self._invalidate_node_embeddings_file()
self._query_embeddings_cache = {}
async def get_cached_nx_graph(self) -> nx.Graph:
"""Get cached NetworkX graph instance to avoid repeated construction"""
if self._cached_nx_graph is None:
logger.info("Building cached NetworkX graph...")
# Build undirected graph for flow diffusion
G = nx.Graph()
# Add all edges
edge_count = 0
for u, v in self._graph.edges():
edge_data = self._graph.edges[u, v]
# Filter out None values to avoid GraphML writer issues
filtered_edge_data = {k: v_val for k, v_val in edge_data.items() if v_val is not None} if edge_data else {}
weight = filtered_edge_data.get('weight', 1.0)
G.add_edge(u, v, weight=weight, **{k: v_val for k, v_val in filtered_edge_data.items() if k != 'weight'})
edge_count += 1
# Add all nodes
node_count = 0
for node, data in self._graph.nodes(data=True):
# Filter out None values to avoid GraphML writer issues
filtered_data = {k: v for k, v in data.items() if v is not None}
G.add_node(node, **filtered_data)
node_count += 1
self._cached_nx_graph = G
logger.info(f"Successfully cached NetworkX graph with {node_count} nodes and {edge_count} edges")
else:
logger.info(f"Using cached NetworkX graph with {self._cached_nx_graph.number_of_nodes()} nodes and {self._cached_nx_graph.number_of_edges()} edges")
return self._cached_nx_graph
async def get_cached_node_embeddings(self, global_config: dict) -> dict:
"""Get node embeddings; prioritize loading from working directory file, compute and persist if not exists.
File path: working_dir/kg_node_embeddings_{namespace}.json
"""
# 1) Try to load from persisted file
try:
if os.path.exists(self._node_embeddings_file):
persisted = load_json(self._node_embeddings_file) or {}
if isinstance(persisted, dict) and len(persisted) > 0:
logger.info(
f"Loaded node embeddings from file ({len(persisted)} nodes): {self._node_embeddings_file}"
)
return persisted
except Exception as e:
logger.warning(
f"Failed to load node embeddings file {self._node_embeddings_file}: {e}"
)
# 2) Compute if not available on disk
logger.info("No persisted node embeddings found, computing new ones...")
if "embedding_func" not in global_config or not global_config["embedding_func"]:
logger.warning("No embedding function available in global config")
return {}
try:
all_nodes = list(self._graph.nodes())
if not all_nodes:
logger.warning("No nodes found in graph for embedding computation")
return {}
logger.info(
f"Preparing to compute embeddings for {len(all_nodes)} nodes..."
)
# Get batch size and token limits
batch_size = global_config.get("embedding_batch_num", 32)
max_tokens_per_request = global_config.get("max_embed_tokens", 8192)
# Prepare node texts
node_texts = []
for node in all_nodes:
node_data = self._graph.nodes.get(node, {})
if node_data and "description" in node_data:
node_text = f"{node} {node_data['description']}"
else:
node_text = node
node_texts.append(node_text)
# Token counting
import tiktoken
tiktoken_model = global_config.get("tiktoken_model_name", "gpt-4o-mini")
try:
encoding = tiktoken.encoding_for_model(tiktoken_model)
except Exception:
encoding = tiktoken.get_encoding("cl100k_base")
all_embeddings = []
for i in range(0, len(node_texts), batch_size):
batch_texts = node_texts[i : i + batch_size]
total_tokens = sum(len(encoding.encode(text)) for text in batch_texts)
if total_tokens > max_tokens_per_request:
logger.warning(
f"Batch {i//batch_size + 1} exceeds token limit ({total_tokens} > {max_tokens_per_request}), reducing batch size..."
)
sub_batch_size = max(1, batch_size // 2)
for j in range(0, len(batch_texts), sub_batch_size):
sub_batch_texts = batch_texts[j : j + sub_batch_size]
sub_total_tokens = sum(
len(encoding.encode(text)) for text in sub_batch_texts
)
if sub_total_tokens > max_tokens_per_request:
logger.warning(
f"Sub-batch still exceeds token limit ({sub_total_tokens} > {max_tokens_per_request}), processing one by one..."
)
for text in sub_batch_texts:
try:
embedding_array = await global_config["embedding_func"](
[text]
)
all_embeddings.append(embedding_array[0])
except Exception as e:
logger.error(
f"Failed to process text for embedding: {e}"
)
all_embeddings.append([0.0] * 1536)
else:
try:
embedding_array = await global_config["embedding_func"](
sub_batch_texts
)
all_embeddings.extend(embedding_array)
except Exception as e:
logger.error(f"Failed to process sub-batch: {e}")
for _ in sub_batch_texts:
all_embeddings.append([0.0] * 1536)
else:
try:
embedding_array = await global_config["embedding_func"](
batch_texts
)
all_embeddings.extend(embedding_array)
except Exception as e:
logger.error(f"Failed to process batch: {e}")
for _ in batch_texts:
all_embeddings.append([0.0] * 1536)
# Map embeddings back to node ids
node_embeddings = {}
for i, node in enumerate(all_nodes):
if i < len(all_embeddings):
emb = all_embeddings[i]
node_embeddings[node] = (
emb.tolist() if hasattr(emb, "tolist") else emb
)
else:
logger.warning(f"Missing embedding for node {node}")
# Persist to disk
try:
write_json(node_embeddings, self._node_embeddings_file)
logger.info(
f"Persisted node embeddings to file: {self._node_embeddings_file} ({len(node_embeddings)} nodes)"
)
except Exception as e:
logger.error(
f"Failed to persist node embeddings to {self._node_embeddings_file}: {e}"
)
return node_embeddings
except Exception as e:
logger.error(f"Failed to compute node embeddings: {e}")
return {}
async def get_cached_query_embedding(self, query: str, global_config: dict) -> list:
"""Get cached query embedding to avoid repeated computation"""
if query not in self._query_embeddings_cache:
logger.info(f"Computing new query embedding for: {query[:50]}...")
if "embedding_func" in global_config and global_config["embedding_func"]:
try:
query_embedding_array = await global_config["embedding_func"]([query])
self._query_embeddings_cache[query] = query_embedding_array[0].tolist()
logger.info(f"Successfully cached query embedding for: {query[:50]}...")
# Limit cache size to avoid excessive memory usage
max_cache_size = 100 # Cache at most 100 query embeddings
if len(self._query_embeddings_cache) > max_cache_size:
# Remove oldest cache entry
oldest_query = next(iter(self._query_embeddings_cache))
del self._query_embeddings_cache[oldest_query]
logger.info(f"Removed oldest query embedding from cache to maintain size limit")
except Exception as e:
logger.error(f"Failed to compute query embedding: {e}")
return None
else:
logger.warning("No embedding function available in global config")
return None
else:
logger.info(f"Using cached query embedding for: {query[:50]}...")
return self._query_embeddings_cache[query]
def get_node_embeddings_file_path(self) -> str:
"""Return the path of persisted node embeddings file for external extraction."""
return self._node_embeddings_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]:
if self._graph.has_edge(source_node_id, target_node_id):
return self._graph.edges[source_node_id, target_node_id]
return None
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 get_node_in_edges(self, source_node_id: str):
if self._graph.has_node(source_node_id):
return list(self._graph.in_edges(source_node_id))
return None
async def get_node_out_edges(self, source_node_id: str):
if self._graph.has_node(source_node_id):
return list(self._graph.out_edges(source_node_id))
return None
async def get_pagerank(self,source_node_id:str):
pagerank_list=nx.pagerank(self._graph)
if source_node_id in pagerank_list:
return pagerank_list[source_node_id]
else:
print("pagerank failed")
async def upsert_node(self, node_id: str, node_data: dict[str, str]):
# Filter out None values to avoid GraphML writer issues
filtered_node_data = {k: v for k, v in node_data.items() if v is not None}
self._graph.add_node(node_id, **filtered_node_data)
# Clear cache as graph has been updated
self._cached_nx_graph = None
self._node_embeddings_cache = {}
self._invalidate_node_embeddings_file()
self._query_embeddings_cache = {}
async def upsert_edge(
self, source_node_id: str, target_node_id: str, edge_data: dict[str, str]
):
# Filter out None values to avoid GraphML writer issues
filtered_edge_data = {k: v for k, v in edge_data.items() if v is not None}
# Check if both nodes exist before adding edge
if not self._graph.has_node(source_node_id):
logger.warning(f"Source node {source_node_id} does not exist, skipping edge creation")
return
if not self._graph.has_node(target_node_id):
logger.warning(f"Target node {target_node_id} does not exist, skipping edge creation")
return
self._graph.add_edge(source_node_id, target_node_id, **filtered_edge_data)
# Clear cache as graph has been updated
self._cached_nx_graph = None
self._node_embeddings_cache = {}
self._invalidate_node_embeddings_file()
self._query_embeddings_cache = {}
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.")
# Clear cache as graph has been updated
self._cached_nx_graph = None
self._node_embeddings_cache = {}
self._invalidate_node_embeddings_file()
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
async def edges(self):
return self._graph.edges()
async def nodes(self):
return self._graph.nodes()
async def get_all_nodes(self):
"""Get all nodes with their data"""
return dict(self._graph.nodes(data=True))
async def remove_duplicate_nodes(self):
"""Remove duplicate nodes that might have been created accidentally"""
nodes_data = await self.get_all_nodes()
seen_nodes = set()
duplicates = []
for node_id, node_data in nodes_data.items():
if node_id in seen_nodes:
duplicates.append(node_id)
else:
seen_nodes.add(node_id)
if duplicates:
logger.warning(f"Found {len(duplicates)} duplicate nodes: {duplicates}")
for node_id in duplicates:
if self._graph.has_node(node_id):
self._graph.remove_node(node_id)
logger.info(f"Removed duplicate node: {node_id}")
# Clear cache as graph has been updated
self._cached_nx_graph = None
self._node_embeddings_cache = {}
self._invalidate_node_embeddings_file()
self._query_embeddings_cache = {}
return len(duplicates)
async def get_graph_stats(self):
"""Get statistics about the graph"""
nodes_data = await self.get_all_nodes()
edges = await self.edges()
edges_list = list(edges) if edges else []
# Count nodes by type
node_types = {}
for node_id, node_data in nodes_data.items():
node_type = node_data.get('entity_type', 'unknown')
node_types[node_type] = node_types.get(node_type, 0) + 1
stats = {
'total_nodes': len(nodes_data),
'total_edges': len(edges_list),
'node_types': node_types,
'sample_nodes': list(nodes_data.keys())[:5] if nodes_data else [],
'sample_edges': edges_list[:5] if edges_list else []
}
return stats |