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use seperate module

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This commit is contained in:
Ken Wiltshire
2024-10-26 19:29:45 -04:00
parent 627776d99b
commit 474fe59a79
3 changed files with 285 additions and 296 deletions
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5
lightrag/kg/__init__.py Normal file
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@@ -0,0 +1,5 @@
from .lightrag import LightRAG as LightRAG, QueryParam as QueryParam
__version__ = "0.0.7"
__author__ = "Zirui Guo"
__url__ = "https://github.com/HKUDS/LightRAG"

278
lightrag/kg/neo4j.py Normal file
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@@ -0,0 +1,278 @@
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 load_json, logger, write_json
from ..base import (
BaseGraphStorage
)
from neo4j import GraphDatabase
# Replace with your actual URI, username, and password
URI = "neo4j://localhost:7687"
USERNAME = "neo4j"
PASSWORD = "your_password"
# Create a driver object
@dataclass
class GraphStorage(BaseGraphStorage):
@staticmethod
def load_nx_graph(file_name) -> nx.Graph:
if os.path.exists(file_name):
return nx.read_graphml(file_name)
return None
def __post_init__(self):
# self._graph = preloaded_graph or nx.Graph()
self._driver = GraphDatabase.driver(URI, auth=(USERNAME, PASSWORD))
self._node_embed_algorithms = {
"node2vec": self._node2vec_embed,
}
async def index_done_callback(self):
print ("KG successfully indexed.")
async def has_node(self, node_id: str) -> bool:
entity_name_label = node_id
with self._driver.session() as session:
return session.read_transaction(self._check_node_exists, entity_name_label)
@staticmethod
def _check_node_exists(tx, label):
query = f"MATCH (n:{label}) RETURN count(n) > 0 AS node_exists"
result = tx.run(query)
return result.single()["node_exists"]
async def has_edge(self, source_node_id: str, target_node_id: str) -> bool:
entity_name_label_source = source_node_id
entity_name_label_target = target_node_id
#hard code relaitionship type
with self._driver.session() as session:
result = session.read_transaction(self._check_edge_existence, entity_name_label_source, entity_name_label_target)
return result
@staticmethod
def _check_edge_existence(tx, label1, label2):
query = (
f"MATCH (a:{label1})-[r]-(b:{label2}) "
"RETURN COUNT(r) > 0 AS edgeExists"
)
result = tx.run(query)
return result.single()["edgeExists"]
def close(self):
self._driver.close()
async def get_node(self, node_id: str) -> Union[dict, None]:
entity_name_label = node_id
with self._driver.session() as session:
result = session.run("MATCH (n:{entity_name_label}) RETURN n".format(entity_name_label=entity_name_label))
for record in result:
return record["n"]
async def node_degree(self, node_id: str) -> int:
entity_name_label = node_id
with self._driver.session() as session:
degree = self._find_node_degree(session, entity_name_label)
return degree
@staticmethod
def _find_node_degree(session, label):
with session.begin_transaction() as tx:
result = tx.run("MATCH (n:`{label}`) RETURN n, size((n)--()) AS degree".format(label=label))
record = result.single()
if record:
return record["degree"]
else:
return None
# degree = session.read_transaction(get_edge_degree, 1, 2)
async def edge_degree(self, src_id: str, tgt_id: str) -> int:
entity_name__label_source = src_id
entity_name_label_target = tgt_id
with self._driver.session() as session:
result = session.run(
"""MATCH (n1:{node_label1})-[r]-(n2:{node_label2})
RETURN count(r) AS degree"""
.format(node_label1=node_label1, node_label2=node_label2)
)
record = result.single()
return record["degree"]
async def get_edge(self, source_node_id: str, target_node_id: str) -> Union[dict, None]:
entity_name__label_source = source_node_id
entity_name_label_target = target_node_id
"""
Find all edges between nodes of two given labels
Args:
source_node_label (str): Label of the source nodes
target_node_label (str): Label of the target nodes
Returns:
list: List of all relationships/edges found
"""
with self._driver.session() as session:
query = f"""
MATCH (source:{entity_name__label_source})-[r]-(target:{entity_name_label_target})
RETURN r
"""
result = session.run(query)
return [record["r"] for record in result]
#upsert_node
async def upsert_node(self, node_id: str, node_data: dict[str, str]):
label = node_id
properties = node_data
"""
Upsert a node with the given label and properties within a transaction.
If a node with the same label exists, it will:
- Update existing properties with new values
- Add new properties that don't exist
If no node exists, creates a new node with all properties.
Args:
label: The node label to search for and apply
properties: Dictionary of node properties
Returns:
Dictionary containing the node's properties after upsert, or None if operation fails
"""
with self._driver.session() as session:
# Execute the upsert within a transaction
result = session.execute_write(
self._do_upsert,
label,
properties
)
return result
@staticmethod
def _do_upsert(tx: Transaction, label: str, properties: Dict[str, Any]):
"""
Static method to perform the actual upsert operation within a transaction
Args:
tx: Neo4j transaction object
label: The node label to search for and apply
properties: Dictionary of node properties
Returns:
Dictionary containing the node's properties after upsert, or None if operation fails
"""
# Create the dynamic property string for SET clause
property_string = ", ".join([
f"n.{key} = ${key}"
for key in properties.keys()
])
# Cypher query that either matches existing node or creates new one
query = f"""
MATCH (n:{label})
WITH n LIMIT 1
CALL {{
WITH n
WHERE n IS NOT NULL
SET {property_string}
RETURN n
UNION
WITH n
WHERE n IS NULL
CREATE (n:{label})
SET {property_string}
RETURN n
}}
RETURN n
"""
# Execute the query with properties as parameters
result = tx.run(query, properties)
record = result.single()
if record:
return dict(record["n"])
return None
async def upsert_edge(self, source_node_id: str, target_node_id: str, edge_data: dict[str, str]) -> None:
source_node_label = source_node_id
target_node_label = target_node_id
"""
Upsert an edge and its properties between two nodes identified by their labels.
Args:
source_node_label (str): Label of the source node (used as identifier)
target_node_label (str): Label of the target node (used as identifier)
edge_properties (dict): Dictionary of properties to set on the edge
"""
with self._driver.session() as session:
session.execute_write(
self._do_upsert_edge,
source_node_label,
target_node_label,
edge_data
)
@staticmethod
def _do_upsert_edge(tx, source_node_label: str, target_node_label: str, edge_properties: Dict[str, Any]) -> None:
"""
Static method to perform the edge upsert within a transaction.
The query will:
1. Match the source and target nodes by their labels
2. Merge the DIRECTED relationship
3. Set all properties on the relationship, updating existing ones and adding new ones
"""
# Convert edge properties to Cypher parameter string
props_string = ", ".join(f"r.{key} = ${key}" for key in edge_properties.keys())
query = """
MATCH (source)
WHERE source.label = $source_node_label
MATCH (target)
WHERE target.label = $target_node_label
MERGE (source)-[r:DIRECTED]->(target)
SET {}
""".format(props_string)
# Prepare parameters dictionary
params = {
"source_node_label": source_node_label,
"target_node_label": target_node_label,
**edge_properties
}
# Execute the query
tx.run(query, params)
async def _node2vec_embed(self):
# async def _node2vec_embed(self):
with self._driver.session() as session:
#Define the Cypher query
options = self.global_config["node2vec_params"]
query = f"""CALL gds.node2vec.stream('myGraph', {**options})
YIELD nodeId, embedding
RETURN nodeId, embedding"""
# Run the query and process the results
results = session.run(query)
for record in results:
node_id = record["nodeId"]
embedding = record["embedding"]
print(f"Node ID: {node_id}, Embedding: {embedding}")
#need to return two lists here.

298
lightrag/storage.py
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@@ -6,6 +6,8 @@ from typing import Any, Union, cast
import networkx as nx import networkx as nx
import numpy as np import numpy as np
from nano_vectordb import NanoVectorDB from nano_vectordb import NanoVectorDB
from kg.neo4j import GraphStorage
from .utils import load_json, logger, write_json from .utils import load_json, logger, write_json
from .base import ( from .base import (
@@ -298,299 +300,3 @@ class NetworkXStorage(BaseGraphStorage):
return embeddings, nodes_ids return embeddings, nodes_ids
@dataclass
class Neo4JStorage(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)
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):
print ("KG successfully indexed.")
# Neo4JStorage.write_nx_graph(self._graph, self._graphml_xml_file)
async def has_node(self, node_id: str) -> bool:
entity_name_label = node_id
with self.driver.session() as session:
return session.read_transaction(self._check_node_exists, entity_name_label)
@staticmethod
def _check_node_exists(tx, label):
query = f"MATCH (n:{label}) RETURN count(n) > 0 AS node_exists"
result = tx.run(query)
return result.single()["node_exists"]
async def has_edge(self, source_node_id: str, target_node_id: str) -> bool:
entity_name_label_source = source_node_id
entity_name_label_target = target_node_id
#hard code relaitionship type
with self.driver.session() as session:
result = session.read_transaction(self._check_edge_existence, entity_name_label_source, entity_name_label_target)
return result
@staticmethod
def _check_edge_existence(tx, label1, label2):
query = (
f"MATCH (a:{label1})-[r]-(b:{label2}) "
"RETURN COUNT(r) > 0 AS edgeExists"
)
result = tx.run(query)
return result.single()["edgeExists"]
def close(self):
self.driver.close()
async def get_node(self, node_id: str) -> Union[dict, None]:
entity_name_label = node_id
with driver.session() as session:
result = session.run(
"MATCH (n) WHERE n.name = $name RETURN n",
name=node_name
)
for record in result:
return record["n"] # Return the first matching node
async def node_degree(self, node_id: str) -> int:
entity_name_label = node_id
neo4j = Neo4j("bolt://localhost:7687", "neo4j", "password")
with neo4j.driver.session() as session:
degree = Neo4j.find_node_degree(session, entity_name_label)
return degree
@staticmethod
def find_node_degree(session, label):
with session.begin_transaction() as tx:
result = tx.run("MATCH (n:`{label}`) RETURN n, size((n)--()) AS degree".format(label=label))
record = result.single()
if record:
return record["degree"]
else:
return None
# edge_degree
# from neo4j import GraphDatabase
async def edge_degree(self, src_id: str, tgt_id: str) -> int:
entity_name__label_source = src_id
entity_name_label_target = tgt_id
with graph_db.session() as session:
result = session.run(
"""MATCH (n1:{node_label1})-[r]-(n2:{node_label2})
RETURN count(r) AS degree"""
.format(node_label1=node_label1, node_label2=node_label2)
)
record = result.single()
return record["degree"]
# driver = GraphDatabase.driver("bolt://localhost:7687", auth=("neo4j", "password"))
#
#
# def edge_degree(tx, source_id, target_id):
# result = tx.run("""
# MATCH (source) WHERE ID(source) = $source_id
# MATCH (target) WHERE ID(target) = $target_id
# MATCH (source)-[r]-(target)
# RETURN COUNT(r) AS degree
# """, source_id=source_id, target_id=target_id)
# return result.single()["degree"]
# with driver.session() as session:
# degree = session.read_transaction(get_edge_degree, 1, 2)
# print("Degree of edge between source and target:", degree)
async def get_edge(self, source_node_id: str, target_node_id: str) -> Union[dict, None]:
entity_name__label_source = src_id
entity_name_label_target = tgt_id
"""
Find all edges between nodes of two given labels
Args:
source_node_label (str): Label of the source nodes
target_node_label (str): Label of the target nodes
Returns:
list: List of all relationships/edges found
"""
with self.driver.session() as session:
query = f"""
MATCH (source:{entity_name__label_source})-[r]-(target:{entity_name_label_target})
RETURN r
"""
result = session.run(query)
return [record["r"] for record in result]
#upsert_node
async def upsert_node(self, node_id: str, node_data: dict[str, str]):
label = node_id
properties = node_data
"""
Upsert a node with the given label and properties within a transaction.
If a node with the same label exists, it will:
- Update existing properties with new values
- Add new properties that don't exist
If no node exists, creates a new node with all properties.
Args:
label: The node label to search for and apply
properties: Dictionary of node properties
Returns:
Dictionary containing the node's properties after upsert, or None if operation fails
"""
with self.driver.session() as session:
# Execute the upsert within a transaction
result = session.execute_write(
self._do_upsert,
label,
properties
)
return result
@staticmethod
def _do_upsert(tx: Transaction, label: str, properties: Dict[str, Any]):
"""
Static method to perform the actual upsert operation within a transaction
Args:
tx: Neo4j transaction object
label: The node label to search for and apply
properties: Dictionary of node properties
Returns:
Dictionary containing the node's properties after upsert, or None if operation fails
"""
# Create the dynamic property string for SET clause
property_string = ", ".join([
f"n.{key} = ${key}"
for key in properties.keys()
])
# Cypher query that either matches existing node or creates new one
query = f"""
MATCH (n:{label})
WITH n LIMIT 1
CALL {{
WITH n
WHERE n IS NOT NULL
SET {property_string}
RETURN n
UNION
WITH n
WHERE n IS NULL
CREATE (n:{label})
SET {property_string}
RETURN n
}}
RETURN n
"""
# Execute the query with properties as parameters
result = tx.run(query, properties)
record = result.single()
if record:
return dict(record["n"])
return None
async def upsert_edge(self, source_node_id: str, target_node_id: str, edge_data: dict[str, str]) -> None:
source_node_label = source_node_id
target_node_label = target_node_id
"""
Upsert an edge and its properties between two nodes identified by their labels.
Args:
source_node_label (str): Label of the source node (used as identifier)
target_node_label (str): Label of the target node (used as identifier)
edge_properties (dict): Dictionary of properties to set on the edge
"""
with self._driver.session() as session:
session.execute_write(
self._do_upsert_edge,
source_node_label,
target_node_label,
edge_data
)
@staticmethod
def _do_upsert_edge(tx, source_node_label: str, target_node_label: str, edge_properties: Dict[str, Any]) -> None:
"""
Static method to perform the edge upsert within a transaction.
The query will:
1. Match the source and target nodes by their labels
2. Merge the DIRECTED relationship
3. Set all properties on the relationship, updating existing ones and adding new ones
"""
# Convert edge properties to Cypher parameter string
props_string = ", ".join(f"r.{key} = ${key}" for key in edge_properties.keys())
query = """
MATCH (source)
WHERE source.label = $source_node_label
MATCH (target)
WHERE target.label = $target_node_label
MERGE (source)-[r:DIRECTED]->(target)
SET {}
""".format(props_string)
# Prepare parameters dictionary
params = {
"source_node_label": source_node_label,
"target_node_label": target_node_label,
**edge_properties
}
# Execute the query
tx.run(query, params)
async def _node2vec_embed(self):
# async def _node2vec_embed(self):
with driver.session() as session:
#Define the Cypher query
options = self.global_config["node2vec_params"]
query = f"""CALL gds.node2vec.stream('myGraph', {**options})
YIELD nodeId, embedding
RETURN nodeId, embedding"""
# Run the query and process the results
results = session.run(query)
for record in results:
node_id = record["nodeId"]
embedding = record["embedding"]
print(f"Node ID: {node_id}, Embedding: {embedding}")
#need to return two lists here.