mirror of
https://github.com/HKUDS/LightRAG.git
synced 2025-07-26 02:10:50 +00:00
1158 lines
48 KiB
Python
1158 lines
48 KiB
Python
import inspect
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import os
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import re
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from dataclasses import dataclass
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from typing import Any, final
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import numpy as np
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import configparser
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from tenacity import (
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retry,
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stop_after_attempt,
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wait_exponential,
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retry_if_exception_type,
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)
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import logging
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from ..utils import logger
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from ..base import BaseGraphStorage
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from ..types import KnowledgeGraph, KnowledgeGraphNode, KnowledgeGraphEdge
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import pipmaster as pm
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if not pm.is_installed("neo4j"):
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pm.install("neo4j")
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from neo4j import ( # type: ignore
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AsyncGraphDatabase,
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exceptions as neo4jExceptions,
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AsyncDriver,
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AsyncManagedTransaction,
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)
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config = configparser.ConfigParser()
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config.read("config.ini", "utf-8")
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# Get maximum number of graph nodes from environment variable, default is 1000
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MAX_GRAPH_NODES = int(os.getenv("MAX_GRAPH_NODES", 1000))
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# Set neo4j logger level to ERROR to suppress warning logs
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logging.getLogger("neo4j").setLevel(logging.ERROR)
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@final
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@dataclass
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class Neo4JStorage(BaseGraphStorage):
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def __init__(self, namespace, global_config, embedding_func):
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super().__init__(
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namespace=namespace,
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global_config=global_config,
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embedding_func=embedding_func,
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)
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self._driver = None
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def __post_init__(self):
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self._node_embed_algorithms = {
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"node2vec": self._node2vec_embed,
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}
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async def initialize(self):
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URI = os.environ.get("NEO4J_URI", config.get("neo4j", "uri", fallback=None))
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USERNAME = os.environ.get(
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"NEO4J_USERNAME", config.get("neo4j", "username", fallback=None)
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)
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PASSWORD = os.environ.get(
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"NEO4J_PASSWORD", config.get("neo4j", "password", fallback=None)
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)
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MAX_CONNECTION_POOL_SIZE = int(
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os.environ.get(
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"NEO4J_MAX_CONNECTION_POOL_SIZE",
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config.get("neo4j", "connection_pool_size", fallback=50),
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)
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)
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CONNECTION_TIMEOUT = float(
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os.environ.get(
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"NEO4J_CONNECTION_TIMEOUT",
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config.get("neo4j", "connection_timeout", fallback=30.0),
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),
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)
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CONNECTION_ACQUISITION_TIMEOUT = float(
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os.environ.get(
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"NEO4J_CONNECTION_ACQUISITION_TIMEOUT",
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config.get("neo4j", "connection_acquisition_timeout", fallback=30.0),
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),
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)
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MAX_TRANSACTION_RETRY_TIME = float(
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os.environ.get(
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"NEO4J_MAX_TRANSACTION_RETRY_TIME",
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config.get("neo4j", "max_transaction_retry_time", fallback=30.0),
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),
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)
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DATABASE = os.environ.get(
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"NEO4J_DATABASE", re.sub(r"[^a-zA-Z0-9-]", "-", self.namespace)
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)
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self._driver: AsyncDriver = AsyncGraphDatabase.driver(
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URI,
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auth=(USERNAME, PASSWORD),
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max_connection_pool_size=MAX_CONNECTION_POOL_SIZE,
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connection_timeout=CONNECTION_TIMEOUT,
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connection_acquisition_timeout=CONNECTION_ACQUISITION_TIMEOUT,
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max_transaction_retry_time=MAX_TRANSACTION_RETRY_TIME,
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)
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# Try to connect to the database and create it if it doesn't exist
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for database in (DATABASE, None):
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self._DATABASE = database
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connected = False
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try:
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async with self._driver.session(database=database) as session:
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try:
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result = await session.run("MATCH (n) RETURN n LIMIT 0")
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await result.consume() # Ensure result is consumed
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logger.info(f"Connected to {database} at {URI}")
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connected = True
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except neo4jExceptions.ServiceUnavailable as e:
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logger.error(
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f"{database} at {URI} is not available".capitalize()
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)
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raise e
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except neo4jExceptions.AuthError as e:
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logger.error(f"Authentication failed for {database} at {URI}")
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raise e
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except neo4jExceptions.ClientError as e:
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if e.code == "Neo.ClientError.Database.DatabaseNotFound":
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logger.info(
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f"{database} at {URI} not found. Try to create specified database.".capitalize()
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)
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try:
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async with self._driver.session() as session:
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result = await session.run(
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f"CREATE DATABASE `{database}` IF NOT EXISTS"
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)
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await result.consume() # Ensure result is consumed
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logger.info(f"{database} at {URI} created".capitalize())
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connected = True
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except (
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neo4jExceptions.ClientError,
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neo4jExceptions.DatabaseError,
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) as e:
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if (
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e.code
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== "Neo.ClientError.Statement.UnsupportedAdministrationCommand"
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) or (e.code == "Neo.DatabaseError.Statement.ExecutionFailed"):
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if database is not None:
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logger.warning(
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"This Neo4j instance does not support creating databases. Try to use Neo4j Desktop/Enterprise version or DozerDB instead. Fallback to use the default database."
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)
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if database is None:
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logger.error(f"Failed to create {database} at {URI}")
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raise e
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if connected:
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# Create index for base nodes on entity_id if it doesn't exist
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try:
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async with self._driver.session(database=database) as session:
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# Check if index exists first
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check_query = """
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CALL db.indexes() YIELD name, labelsOrTypes, properties
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WHERE labelsOrTypes = ['base'] AND properties = ['entity_id']
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RETURN count(*) > 0 AS exists
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"""
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try:
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check_result = await session.run(check_query)
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record = await check_result.single()
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await check_result.consume()
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index_exists = record and record.get("exists", False)
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if not index_exists:
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# Create index only if it doesn't exist
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result = await session.run(
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"CREATE INDEX FOR (n:base) ON (n.entity_id)"
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)
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await result.consume()
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logger.info(
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f"Created index for base nodes on entity_id in {database}"
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)
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except Exception:
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# Fallback if db.indexes() is not supported in this Neo4j version
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result = await session.run(
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"CREATE INDEX IF NOT EXISTS FOR (n:base) ON (n.entity_id)"
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)
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await result.consume()
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except Exception as e:
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logger.warning(f"Failed to create index: {str(e)}")
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break
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async def finalize(self):
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"""Close the Neo4j driver and release all resources"""
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if self._driver:
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await self._driver.close()
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self._driver = None
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async def __aexit__(self, exc_type, exc, tb):
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"""Ensure driver is closed when context manager exits"""
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await self.finalize()
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async def index_done_callback(self) -> None:
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# Noe4J handles persistence automatically
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pass
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async def has_node(self, node_id: str) -> bool:
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"""
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Check if a node with the given label exists in the database
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Args:
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node_id: Label of the node to check
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Returns:
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bool: True if node exists, False otherwise
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Raises:
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ValueError: If node_id is invalid
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Exception: If there is an error executing the query
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"""
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async with self._driver.session(
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database=self._DATABASE, default_access_mode="READ"
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) as session:
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try:
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query = "MATCH (n:base {entity_id: $entity_id}) RETURN count(n) > 0 AS node_exists"
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result = await session.run(query, entity_id=node_id)
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single_result = await result.single()
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await result.consume() # Ensure result is fully consumed
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return single_result["node_exists"]
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except Exception as e:
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logger.error(f"Error checking node existence for {node_id}: {str(e)}")
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await result.consume() # Ensure results are consumed even on error
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raise
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async def has_edge(self, source_node_id: str, target_node_id: str) -> bool:
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"""
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Check if an edge exists between two nodes
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Args:
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source_node_id: Label of the source node
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target_node_id: Label of the target node
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Returns:
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bool: True if edge exists, False otherwise
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Raises:
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ValueError: If either node_id is invalid
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Exception: If there is an error executing the query
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"""
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async with self._driver.session(
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database=self._DATABASE, default_access_mode="READ"
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) as session:
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try:
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query = (
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"MATCH (a:base {entity_id: $source_entity_id})-[r]-(b:base {entity_id: $target_entity_id}) "
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"RETURN COUNT(r) > 0 AS edgeExists"
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)
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result = await session.run(
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query,
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source_entity_id=source_node_id,
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target_entity_id=target_node_id,
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)
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single_result = await result.single()
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await result.consume() # Ensure result is fully consumed
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return single_result["edgeExists"]
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except Exception as e:
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logger.error(
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f"Error checking edge existence between {source_node_id} and {target_node_id}: {str(e)}"
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)
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await result.consume() # Ensure results are consumed even on error
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raise
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async def get_node(self, node_id: str) -> dict[str, str] | None:
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"""Get node by its label identifier, return only node properties
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Args:
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node_id: The node label to look up
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Returns:
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dict: Node properties if found
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None: If node not found
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Raises:
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ValueError: If node_id is invalid
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Exception: If there is an error executing the query
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"""
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async with self._driver.session(
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database=self._DATABASE, default_access_mode="READ"
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) as session:
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try:
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query = "MATCH (n:base {entity_id: $entity_id}) RETURN n"
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result = await session.run(query, entity_id=node_id)
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try:
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records = await result.fetch(
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2
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) # Get 2 records for duplication check
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if len(records) > 1:
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logger.warning(
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f"Multiple nodes found with label '{node_id}'. Using first node."
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)
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if records:
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node = records[0]["n"]
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node_dict = dict(node)
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# Remove base label from labels list if it exists
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if "labels" in node_dict:
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node_dict["labels"] = [
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label
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for label in node_dict["labels"]
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if label != "base"
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]
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logger.debug(f"Neo4j query node {query} return: {node_dict}")
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return node_dict
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return None
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finally:
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await result.consume() # Ensure result is fully consumed
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except Exception as e:
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logger.error(f"Error getting node for {node_id}: {str(e)}")
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raise
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async def node_degree(self, node_id: str) -> int:
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"""Get the degree (number of relationships) of a node with the given label.
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If multiple nodes have the same label, returns the degree of the first node.
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If no node is found, returns 0.
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Args:
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node_id: The label of the node
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Returns:
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int: The number of relationships the node has, or 0 if no node found
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||
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||
Raises:
|
||
ValueError: If node_id is invalid
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||
Exception: If there is an error executing the query
|
||
"""
|
||
async with self._driver.session(
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database=self._DATABASE, default_access_mode="READ"
|
||
) as session:
|
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try:
|
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query = """
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MATCH (n:base {entity_id: $entity_id})
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OPTIONAL MATCH (n)-[r]-()
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RETURN COUNT(r) AS degree
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"""
|
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result = await session.run(query, entity_id=node_id)
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try:
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record = await result.single()
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||
|
||
if not record:
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logger.warning(f"No node found with label '{node_id}'")
|
||
return 0
|
||
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||
degree = record["degree"]
|
||
logger.debug(
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f"Neo4j query node degree for {node_id} return: {degree}"
|
||
)
|
||
return degree
|
||
finally:
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await result.consume() # Ensure result is fully consumed
|
||
except Exception as e:
|
||
logger.error(f"Error getting node degree for {node_id}: {str(e)}")
|
||
raise
|
||
|
||
async def edge_degree(self, src_id: str, tgt_id: str) -> int:
|
||
"""Get the total degree (sum of relationships) of two nodes.
|
||
|
||
Args:
|
||
src_id: Label of the source node
|
||
tgt_id: Label of the target node
|
||
|
||
Returns:
|
||
int: Sum of the degrees of both nodes
|
||
"""
|
||
src_degree = await self.node_degree(src_id)
|
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trg_degree = await self.node_degree(tgt_id)
|
||
|
||
# Convert None to 0 for addition
|
||
src_degree = 0 if src_degree is None else src_degree
|
||
trg_degree = 0 if trg_degree is None else trg_degree
|
||
|
||
degrees = int(src_degree) + int(trg_degree)
|
||
return degrees
|
||
|
||
async def get_edge(
|
||
self, source_node_id: str, target_node_id: str
|
||
) -> dict[str, str] | None:
|
||
"""Get edge properties between two nodes.
|
||
|
||
Args:
|
||
source_node_id: Label of the source node
|
||
target_node_id: Label of the target node
|
||
|
||
Returns:
|
||
dict: Edge properties if found, default properties if not found or on error
|
||
|
||
Raises:
|
||
ValueError: If either node_id is invalid
|
||
Exception: If there is an error executing the query
|
||
"""
|
||
try:
|
||
async with self._driver.session(
|
||
database=self._DATABASE, default_access_mode="READ"
|
||
) as session:
|
||
query = """
|
||
MATCH (start:base {entity_id: $source_entity_id})-[r]-(end:base {entity_id: $target_entity_id})
|
||
RETURN properties(r) as edge_properties
|
||
"""
|
||
result = await session.run(
|
||
query,
|
||
source_entity_id=source_node_id,
|
||
target_entity_id=target_node_id,
|
||
)
|
||
try:
|
||
records = await result.fetch(2)
|
||
|
||
if len(records) > 1:
|
||
logger.warning(
|
||
f"Multiple edges found between '{source_node_id}' and '{target_node_id}'. Using first edge."
|
||
)
|
||
if records:
|
||
try:
|
||
edge_result = dict(records[0]["edge_properties"])
|
||
logger.debug(f"Result: {edge_result}")
|
||
# Ensure required keys exist with defaults
|
||
required_keys = {
|
||
"weight": 0.0,
|
||
"source_id": None,
|
||
"description": None,
|
||
"keywords": None,
|
||
}
|
||
for key, default_value in required_keys.items():
|
||
if key not in edge_result:
|
||
edge_result[key] = default_value
|
||
logger.warning(
|
||
f"Edge between {source_node_id} and {target_node_id} "
|
||
f"missing {key}, using default: {default_value}"
|
||
)
|
||
|
||
logger.debug(
|
||
f"{inspect.currentframe().f_code.co_name}:query:{query}:result:{edge_result}"
|
||
)
|
||
return edge_result
|
||
except (KeyError, TypeError, ValueError) as e:
|
||
logger.error(
|
||
f"Error processing edge properties between {source_node_id} "
|
||
f"and {target_node_id}: {str(e)}"
|
||
)
|
||
# Return default edge properties on error
|
||
return {
|
||
"weight": 0.0,
|
||
"source_id": None,
|
||
"description": None,
|
||
"keywords": None,
|
||
}
|
||
|
||
logger.debug(
|
||
f"{inspect.currentframe().f_code.co_name}: No edge found between {source_node_id} and {target_node_id}"
|
||
)
|
||
# Return None when no edge found
|
||
return None
|
||
finally:
|
||
await result.consume() # Ensure result is fully consumed
|
||
|
||
except Exception as e:
|
||
logger.error(
|
||
f"Error in get_edge between {source_node_id} and {target_node_id}: {str(e)}"
|
||
)
|
||
raise
|
||
|
||
async def get_node_edges(self, source_node_id: str) -> list[tuple[str, str]] | None:
|
||
"""Retrieves all edges (relationships) for a particular node identified by its label.
|
||
|
||
Args:
|
||
source_node_id: Label of the node to get edges for
|
||
|
||
Returns:
|
||
list[tuple[str, str]]: List of (source_label, target_label) tuples representing edges
|
||
None: If no edges found
|
||
|
||
Raises:
|
||
ValueError: If source_node_id is invalid
|
||
Exception: If there is an error executing the query
|
||
"""
|
||
try:
|
||
async with self._driver.session(
|
||
database=self._DATABASE, default_access_mode="READ"
|
||
) as session:
|
||
try:
|
||
query = """MATCH (n:base {entity_id: $entity_id})
|
||
OPTIONAL MATCH (n)-[r]-(connected:base)
|
||
WHERE connected.entity_id IS NOT NULL
|
||
RETURN n, r, connected"""
|
||
results = await session.run(query, entity_id=source_node_id)
|
||
|
||
edges = []
|
||
async for record in results:
|
||
source_node = record["n"]
|
||
connected_node = record["connected"]
|
||
|
||
# Skip if either node is None
|
||
if not source_node or not connected_node:
|
||
continue
|
||
|
||
source_label = (
|
||
source_node.get("entity_id")
|
||
if source_node.get("entity_id")
|
||
else None
|
||
)
|
||
target_label = (
|
||
connected_node.get("entity_id")
|
||
if connected_node.get("entity_id")
|
||
else None
|
||
)
|
||
|
||
if source_label and target_label:
|
||
edges.append((source_label, target_label))
|
||
|
||
await results.consume() # Ensure results are consumed
|
||
return edges
|
||
except Exception as e:
|
||
logger.error(
|
||
f"Error getting edges for node {source_node_id}: {str(e)}"
|
||
)
|
||
await results.consume() # Ensure results are consumed even on error
|
||
raise
|
||
except Exception as e:
|
||
logger.error(f"Error in get_node_edges for {source_node_id}: {str(e)}")
|
||
raise
|
||
|
||
@retry(
|
||
stop=stop_after_attempt(3),
|
||
wait=wait_exponential(multiplier=1, min=4, max=10),
|
||
retry=retry_if_exception_type(
|
||
(
|
||
neo4jExceptions.ServiceUnavailable,
|
||
neo4jExceptions.TransientError,
|
||
neo4jExceptions.WriteServiceUnavailable,
|
||
neo4jExceptions.ClientError,
|
||
)
|
||
),
|
||
)
|
||
async def upsert_node(self, node_id: str, node_data: dict[str, str]) -> None:
|
||
"""
|
||
Upsert a node in the Neo4j database.
|
||
|
||
Args:
|
||
node_id: The unique identifier for the node (used as label)
|
||
node_data: Dictionary of node properties
|
||
"""
|
||
properties = node_data
|
||
entity_type = properties["entity_type"]
|
||
if "entity_id" not in properties:
|
||
raise ValueError("Neo4j: node properties must contain an 'entity_id' field")
|
||
|
||
try:
|
||
async with self._driver.session(database=self._DATABASE) as session:
|
||
|
||
async def execute_upsert(tx: AsyncManagedTransaction):
|
||
query = (
|
||
"""
|
||
MERGE (n:base {entity_id: $entity_id})
|
||
SET n += $properties
|
||
SET n:`%s`
|
||
"""
|
||
% entity_type
|
||
)
|
||
result = await tx.run(
|
||
query, entity_id=node_id, properties=properties
|
||
)
|
||
logger.debug(
|
||
f"Upserted node with entity_id '{node_id}' and properties: {properties}"
|
||
)
|
||
await result.consume() # Ensure result is fully consumed
|
||
|
||
await session.execute_write(execute_upsert)
|
||
except Exception as e:
|
||
logger.error(f"Error during upsert: {str(e)}")
|
||
raise
|
||
|
||
@retry(
|
||
stop=stop_after_attempt(3),
|
||
wait=wait_exponential(multiplier=1, min=4, max=10),
|
||
retry=retry_if_exception_type(
|
||
(
|
||
neo4jExceptions.ServiceUnavailable,
|
||
neo4jExceptions.TransientError,
|
||
neo4jExceptions.WriteServiceUnavailable,
|
||
neo4jExceptions.ClientError,
|
||
)
|
||
),
|
||
)
|
||
async def upsert_edge(
|
||
self, source_node_id: str, target_node_id: str, edge_data: dict[str, str]
|
||
) -> None:
|
||
"""
|
||
Upsert an edge and its properties between two nodes identified by their labels.
|
||
Ensures both source and target nodes exist and are unique before creating the edge.
|
||
Uses entity_id property to uniquely identify nodes.
|
||
|
||
Args:
|
||
source_node_id (str): Label of the source node (used as identifier)
|
||
target_node_id (str): Label of the target node (used as identifier)
|
||
edge_data (dict): Dictionary of properties to set on the edge
|
||
|
||
Raises:
|
||
ValueError: If either source or target node does not exist or is not unique
|
||
"""
|
||
try:
|
||
edge_properties = edge_data
|
||
async with self._driver.session(database=self._DATABASE) as session:
|
||
|
||
async def execute_upsert(tx: AsyncManagedTransaction):
|
||
query = """
|
||
MATCH (source:base {entity_id: $source_entity_id})
|
||
WITH source
|
||
MATCH (target:base {entity_id: $target_entity_id})
|
||
MERGE (source)-[r:DIRECTED]-(target)
|
||
SET r += $properties
|
||
RETURN r, source, target
|
||
"""
|
||
result = await tx.run(
|
||
query,
|
||
source_entity_id=source_node_id,
|
||
target_entity_id=target_node_id,
|
||
properties=edge_properties,
|
||
)
|
||
try:
|
||
records = await result.fetch(2)
|
||
if records:
|
||
logger.debug(
|
||
f"Upserted edge from '{source_node_id}' to '{target_node_id}'"
|
||
f"with properties: {edge_properties}"
|
||
)
|
||
finally:
|
||
await result.consume() # Ensure result is consumed
|
||
|
||
await session.execute_write(execute_upsert)
|
||
except Exception as e:
|
||
logger.error(f"Error during edge upsert: {str(e)}")
|
||
raise
|
||
|
||
async def _node2vec_embed(self):
|
||
print("Implemented but never called.")
|
||
|
||
async def get_knowledge_graph(
|
||
self,
|
||
node_label: str,
|
||
max_depth: int = 3,
|
||
max_nodes: int = MAX_GRAPH_NODES,
|
||
) -> KnowledgeGraph:
|
||
"""
|
||
Retrieve a connected subgraph of nodes where the label includes the specified `node_label`.
|
||
|
||
Args:
|
||
node_label: Label of the starting node, * means all nodes
|
||
max_depth: Maximum depth of the subgraph, Defaults to 3
|
||
max_nodes: Maxiumu nodes to return by BFS, Defaults to 1000
|
||
|
||
Returns:
|
||
KnowledgeGraph object containing nodes and edges, with an is_truncated flag
|
||
indicating whether the graph was truncated due to max_nodes limit
|
||
"""
|
||
result = KnowledgeGraph()
|
||
seen_nodes = set()
|
||
seen_edges = set()
|
||
|
||
async with self._driver.session(
|
||
database=self._DATABASE, default_access_mode="READ"
|
||
) as session:
|
||
try:
|
||
if node_label == "*":
|
||
# First check total node count to determine if graph is truncated
|
||
count_query = "MATCH (n) RETURN count(n) as total"
|
||
count_result = None
|
||
try:
|
||
count_result = await session.run(count_query)
|
||
count_record = await count_result.single()
|
||
|
||
if count_record and count_record["total"] > max_nodes:
|
||
result.is_truncated = True
|
||
logger.info(
|
||
f"Graph truncated: {count_record['total']} nodes found, limited to {max_nodes}"
|
||
)
|
||
finally:
|
||
if count_result:
|
||
await count_result.consume()
|
||
|
||
# Run main query to get nodes with highest degree
|
||
main_query = """
|
||
MATCH (n)
|
||
OPTIONAL MATCH (n)-[r]-()
|
||
WITH n, COALESCE(count(r), 0) AS degree
|
||
ORDER BY degree DESC
|
||
LIMIT $max_nodes
|
||
WITH collect({node: n}) AS filtered_nodes
|
||
UNWIND filtered_nodes AS node_info
|
||
WITH collect(node_info.node) AS kept_nodes, filtered_nodes
|
||
OPTIONAL MATCH (a)-[r]-(b)
|
||
WHERE a IN kept_nodes AND b IN kept_nodes
|
||
RETURN filtered_nodes AS node_info,
|
||
collect(DISTINCT r) AS relationships
|
||
"""
|
||
result_set = None
|
||
try:
|
||
result_set = await session.run(
|
||
main_query,
|
||
{"max_nodes": max_nodes},
|
||
)
|
||
record = await result_set.single()
|
||
finally:
|
||
if result_set:
|
||
await result_set.consume()
|
||
|
||
else:
|
||
# return await self._robust_fallback(node_label, max_depth, max_nodes)
|
||
# First try without limit to check if we need to truncate
|
||
full_query = """
|
||
MATCH (start)
|
||
WHERE start.entity_id = $entity_id
|
||
WITH start
|
||
CALL apoc.path.subgraphAll(start, {
|
||
relationshipFilter: '',
|
||
minLevel: 0,
|
||
maxLevel: $max_depth,
|
||
bfs: true
|
||
})
|
||
YIELD nodes, relationships
|
||
WITH nodes, relationships, size(nodes) AS total_nodes
|
||
UNWIND nodes AS node
|
||
WITH collect({node: node}) AS node_info, relationships, total_nodes
|
||
RETURN node_info, relationships, total_nodes
|
||
"""
|
||
|
||
# Try to get full result
|
||
full_result = None
|
||
try:
|
||
full_result = await session.run(
|
||
full_query,
|
||
{
|
||
"entity_id": node_label,
|
||
"max_depth": max_depth,
|
||
},
|
||
)
|
||
full_record = await full_result.single()
|
||
|
||
# If no record found, return empty KnowledgeGraph
|
||
if not full_record:
|
||
logger.debug(f"No nodes found for entity_id: {node_label}")
|
||
return result
|
||
|
||
# If record found, check node count
|
||
total_nodes = full_record["total_nodes"]
|
||
|
||
if total_nodes <= max_nodes:
|
||
# If node count is within limit, use full result directly
|
||
logger.debug(
|
||
f"Using full result with {total_nodes} nodes (no truncation needed)"
|
||
)
|
||
record = full_record
|
||
else:
|
||
# If node count exceeds limit, set truncated flag and run limited query
|
||
result.is_truncated = True
|
||
logger.info(
|
||
f"Graph truncated: {total_nodes} nodes found, breadth-first search limited to {max_nodes}"
|
||
)
|
||
|
||
# Run limited query
|
||
limited_query = """
|
||
MATCH (start)
|
||
WHERE start.entity_id = $entity_id
|
||
WITH start
|
||
CALL apoc.path.subgraphAll(start, {
|
||
relationshipFilter: '',
|
||
minLevel: 0,
|
||
maxLevel: $max_depth,
|
||
limit: $max_nodes,
|
||
bfs: true
|
||
})
|
||
YIELD nodes, relationships
|
||
UNWIND nodes AS node
|
||
WITH collect({node: node}) AS node_info, relationships
|
||
RETURN node_info, relationships
|
||
"""
|
||
result_set = None
|
||
try:
|
||
result_set = await session.run(
|
||
limited_query,
|
||
{
|
||
"entity_id": node_label,
|
||
"max_depth": max_depth,
|
||
"max_nodes": max_nodes,
|
||
},
|
||
)
|
||
record = await result_set.single()
|
||
finally:
|
||
if result_set:
|
||
await result_set.consume()
|
||
finally:
|
||
if full_result:
|
||
await full_result.consume()
|
||
|
||
if record:
|
||
# Handle nodes (compatible with multi-label cases)
|
||
for node_info in record["node_info"]:
|
||
node = node_info["node"]
|
||
node_id = node.id
|
||
if node_id not in seen_nodes:
|
||
result.nodes.append(
|
||
KnowledgeGraphNode(
|
||
id=f"{node_id}",
|
||
labels=[node.get("entity_id")],
|
||
properties=dict(node),
|
||
)
|
||
)
|
||
seen_nodes.add(node_id)
|
||
|
||
# Handle relationships (including direction information)
|
||
for rel in record["relationships"]:
|
||
edge_id = rel.id
|
||
if edge_id not in seen_edges:
|
||
start = rel.start_node
|
||
end = rel.end_node
|
||
result.edges.append(
|
||
KnowledgeGraphEdge(
|
||
id=f"{edge_id}",
|
||
type=rel.type,
|
||
source=f"{start.id}",
|
||
target=f"{end.id}",
|
||
properties=dict(rel),
|
||
)
|
||
)
|
||
seen_edges.add(edge_id)
|
||
|
||
logger.info(
|
||
f"Subgraph query successful | Node count: {len(result.nodes)} | Edge count: {len(result.edges)}"
|
||
)
|
||
|
||
except neo4jExceptions.ClientError as e:
|
||
logger.warning(f"APOC plugin error: {str(e)}")
|
||
if node_label != "*":
|
||
logger.warning(
|
||
"Neo4j: falling back to basic Cypher recursive search..."
|
||
)
|
||
return await self._robust_fallback(node_label, max_depth, max_nodes)
|
||
else:
|
||
logger.warning(
|
||
"Neo4j: APOC plugin error with wildcard query, returning empty result"
|
||
)
|
||
|
||
return result
|
||
|
||
async def _robust_fallback(
|
||
self, node_label: str, max_depth: int, max_nodes: int
|
||
) -> KnowledgeGraph:
|
||
"""
|
||
Fallback implementation when APOC plugin is not available or incompatible.
|
||
This method implements the same functionality as get_knowledge_graph but uses
|
||
only basic Cypher queries and true breadth-first traversal instead of APOC procedures.
|
||
"""
|
||
from collections import deque
|
||
|
||
result = KnowledgeGraph()
|
||
visited_nodes = set()
|
||
visited_edges = set()
|
||
visited_edge_pairs = set() # 用于跟踪已处理的边对(排序后的source_id, target_id)
|
||
|
||
# Get the starting node's data
|
||
async with self._driver.session(
|
||
database=self._DATABASE, default_access_mode="READ"
|
||
) as session:
|
||
query = """
|
||
MATCH (n:base {entity_id: $entity_id})
|
||
RETURN id(n) as node_id, n
|
||
"""
|
||
node_result = await session.run(query, entity_id=node_label)
|
||
try:
|
||
node_record = await node_result.single()
|
||
if not node_record:
|
||
return result
|
||
|
||
# Create initial KnowledgeGraphNode
|
||
start_node = KnowledgeGraphNode(
|
||
id=f"{node_record['n'].get('entity_id')}",
|
||
labels=[node_record["n"].get("entity_id")],
|
||
properties=dict(node_record["n"]._properties),
|
||
)
|
||
finally:
|
||
await node_result.consume() # Ensure results are consumed
|
||
|
||
# Initialize queue for BFS with (node, edge, depth) tuples
|
||
# edge is None for the starting node
|
||
queue = deque([(start_node, None, 0)])
|
||
|
||
# True BFS implementation using a queue
|
||
while queue and len(visited_nodes) < max_nodes:
|
||
# Dequeue the next node to process
|
||
current_node, current_edge, current_depth = queue.popleft()
|
||
|
||
# Skip if already visited or exceeds max depth
|
||
if current_node.id in visited_nodes:
|
||
continue
|
||
|
||
if current_depth > max_depth:
|
||
logger.debug(
|
||
f"Skipping node at depth {current_depth} (max_depth: {max_depth})"
|
||
)
|
||
continue
|
||
|
||
# Add current node to result
|
||
result.nodes.append(current_node)
|
||
visited_nodes.add(current_node.id)
|
||
|
||
# Add edge to result if it exists and not already added
|
||
if current_edge and current_edge.id not in visited_edges:
|
||
result.edges.append(current_edge)
|
||
visited_edges.add(current_edge.id)
|
||
|
||
# Stop if we've reached the node limit
|
||
if len(visited_nodes) >= max_nodes:
|
||
result.is_truncated = True
|
||
logger.info(
|
||
f"Graph truncated: breadth-first search limited to: {max_nodes} nodes"
|
||
)
|
||
break
|
||
|
||
# Get all edges and target nodes for the current node (even at max_depth)
|
||
async with self._driver.session(
|
||
database=self._DATABASE, default_access_mode="READ"
|
||
) as session:
|
||
query = """
|
||
MATCH (a:base {entity_id: $entity_id})-[r]-(b)
|
||
WITH r, b, id(r) as edge_id, id(b) as target_id
|
||
RETURN r, b, edge_id, target_id
|
||
"""
|
||
results = await session.run(query, entity_id=current_node.id)
|
||
|
||
# Get all records and release database connection
|
||
records = await results.fetch(1000) # Max neighbor nodes we can handle
|
||
await results.consume() # Ensure results are consumed
|
||
|
||
# Process all neighbors - capture all edges but only queue unvisited nodes
|
||
for record in records:
|
||
rel = record["r"]
|
||
edge_id = str(record["edge_id"])
|
||
|
||
if edge_id not in visited_edges:
|
||
b_node = record["b"]
|
||
target_id = b_node.get("entity_id")
|
||
|
||
if target_id: # Only process if target node has entity_id
|
||
# Create KnowledgeGraphNode for target
|
||
target_node = KnowledgeGraphNode(
|
||
id=f"{target_id}",
|
||
labels=[target_id],
|
||
properties=dict(b_node._properties),
|
||
)
|
||
|
||
# Create KnowledgeGraphEdge
|
||
target_edge = KnowledgeGraphEdge(
|
||
id=f"{edge_id}",
|
||
type=rel.type,
|
||
source=f"{current_node.id}",
|
||
target=f"{target_id}",
|
||
properties=dict(rel),
|
||
)
|
||
|
||
# 对source_id和target_id进行排序,确保(A,B)和(B,A)被视为同一条边
|
||
sorted_pair = tuple(sorted([current_node.id, target_id]))
|
||
|
||
# 检查是否已存在相同的边(考虑无向性)
|
||
if sorted_pair not in visited_edge_pairs:
|
||
# 只有当目标节点已经在结果中或将被添加到结果中时,才添加边
|
||
if target_id in visited_nodes or (
|
||
target_id not in visited_nodes
|
||
and current_depth < max_depth
|
||
):
|
||
result.edges.append(target_edge)
|
||
visited_edges.add(edge_id)
|
||
visited_edge_pairs.add(sorted_pair)
|
||
|
||
# Only add unvisited nodes to the queue for further expansion
|
||
if target_id not in visited_nodes:
|
||
# Only add to queue if we're not at max depth yet
|
||
if current_depth < max_depth:
|
||
# Add node to queue with incremented depth
|
||
# Edge is already added to result, so we pass None as edge
|
||
queue.append((target_node, None, current_depth + 1))
|
||
else:
|
||
# At max depth, we've already added the edge but we don't add the node
|
||
# This prevents adding nodes beyond max_depth to the result
|
||
logger.debug(
|
||
f"Node {target_id} beyond max depth {max_depth}, edge added but node not included"
|
||
)
|
||
else:
|
||
# If target node already exists in result, we don't need to add it again
|
||
logger.debug(
|
||
f"Node {target_id} already visited, edge added but node not queued"
|
||
)
|
||
else:
|
||
logger.warning(
|
||
f"Skipping edge {edge_id} due to missing entity_id on target node"
|
||
)
|
||
|
||
logger.info(
|
||
f"BFS subgraph query successful | Node count: {len(result.nodes)} | Edge count: {len(result.edges)}"
|
||
)
|
||
return result
|
||
|
||
async def get_all_labels(self) -> list[str]:
|
||
"""
|
||
Get all existing node labels in the database
|
||
Returns:
|
||
["Person", "Company", ...] # Alphabetically sorted label list
|
||
"""
|
||
async with self._driver.session(
|
||
database=self._DATABASE, default_access_mode="READ"
|
||
) as session:
|
||
# Method 1: Direct metadata query (Available for Neo4j 4.3+)
|
||
# query = "CALL db.labels() YIELD label RETURN label"
|
||
|
||
# Method 2: Query compatible with older versions
|
||
query = """
|
||
MATCH (n:base)
|
||
WHERE n.entity_id IS NOT NULL
|
||
RETURN DISTINCT n.entity_id AS label
|
||
ORDER BY label
|
||
"""
|
||
result = await session.run(query)
|
||
labels = []
|
||
try:
|
||
async for record in result:
|
||
labels.append(record["label"])
|
||
finally:
|
||
await (
|
||
result.consume()
|
||
) # Ensure results are consumed even if processing fails
|
||
return labels
|
||
|
||
@retry(
|
||
stop=stop_after_attempt(3),
|
||
wait=wait_exponential(multiplier=1, min=4, max=10),
|
||
retry=retry_if_exception_type(
|
||
(
|
||
neo4jExceptions.ServiceUnavailable,
|
||
neo4jExceptions.TransientError,
|
||
neo4jExceptions.WriteServiceUnavailable,
|
||
neo4jExceptions.ClientError,
|
||
)
|
||
),
|
||
)
|
||
async def delete_node(self, node_id: str) -> None:
|
||
"""Delete a node with the specified label
|
||
|
||
Args:
|
||
node_id: The label of the node to delete
|
||
"""
|
||
|
||
async def _do_delete(tx: AsyncManagedTransaction):
|
||
query = """
|
||
MATCH (n:base {entity_id: $entity_id})
|
||
DETACH DELETE n
|
||
"""
|
||
result = await tx.run(query, entity_id=node_id)
|
||
logger.debug(f"Deleted node with label '{node_id}'")
|
||
await result.consume() # Ensure result is fully consumed
|
||
|
||
try:
|
||
async with self._driver.session(database=self._DATABASE) as session:
|
||
await session.execute_write(_do_delete)
|
||
except Exception as e:
|
||
logger.error(f"Error during node deletion: {str(e)}")
|
||
raise
|
||
|
||
@retry(
|
||
stop=stop_after_attempt(3),
|
||
wait=wait_exponential(multiplier=1, min=4, max=10),
|
||
retry=retry_if_exception_type(
|
||
(
|
||
neo4jExceptions.ServiceUnavailable,
|
||
neo4jExceptions.TransientError,
|
||
neo4jExceptions.WriteServiceUnavailable,
|
||
neo4jExceptions.ClientError,
|
||
)
|
||
),
|
||
)
|
||
async def remove_nodes(self, nodes: list[str]):
|
||
"""Delete multiple nodes
|
||
|
||
Args:
|
||
nodes: List of node labels to be deleted
|
||
"""
|
||
for node in nodes:
|
||
await self.delete_node(node)
|
||
|
||
@retry(
|
||
stop=stop_after_attempt(3),
|
||
wait=wait_exponential(multiplier=1, min=4, max=10),
|
||
retry=retry_if_exception_type(
|
||
(
|
||
neo4jExceptions.ServiceUnavailable,
|
||
neo4jExceptions.TransientError,
|
||
neo4jExceptions.WriteServiceUnavailable,
|
||
neo4jExceptions.ClientError,
|
||
)
|
||
),
|
||
)
|
||
async def remove_edges(self, edges: list[tuple[str, str]]):
|
||
"""Delete multiple edges
|
||
|
||
Args:
|
||
edges: List of edges to be deleted, each edge is a (source, target) tuple
|
||
"""
|
||
for source, target in edges:
|
||
|
||
async def _do_delete_edge(tx: AsyncManagedTransaction):
|
||
query = """
|
||
MATCH (source:base {entity_id: $source_entity_id})-[r]-(target:base {entity_id: $target_entity_id})
|
||
DELETE r
|
||
"""
|
||
result = await tx.run(
|
||
query, source_entity_id=source, target_entity_id=target
|
||
)
|
||
logger.debug(f"Deleted edge from '{source}' to '{target}'")
|
||
await result.consume() # Ensure result is fully consumed
|
||
|
||
try:
|
||
async with self._driver.session(database=self._DATABASE) as session:
|
||
await session.execute_write(_do_delete_edge)
|
||
except Exception as e:
|
||
logger.error(f"Error during edge deletion: {str(e)}")
|
||
raise
|
||
|
||
async def embed_nodes(
|
||
self, algorithm: str
|
||
) -> tuple[np.ndarray[Any, Any], list[str]]:
|
||
raise NotImplementedError
|
||
|
||
async def drop(self) -> dict[str, str]:
|
||
"""Drop all data from storage and clean up resources
|
||
|
||
This method will delete all nodes and relationships in the Neo4j database.
|
||
|
||
Returns:
|
||
dict[str, str]: Operation status and message
|
||
- On success: {"status": "success", "message": "data dropped"}
|
||
- On failure: {"status": "error", "message": "<error details>"}
|
||
"""
|
||
try:
|
||
async with self._driver.session(database=self._DATABASE) as session:
|
||
# Delete all nodes and relationships
|
||
query = "MATCH (n) DETACH DELETE n"
|
||
result = await session.run(query)
|
||
await result.consume() # Ensure result is fully consumed
|
||
|
||
logger.info(
|
||
f"Process {os.getpid()} drop Neo4j database {self._DATABASE}"
|
||
)
|
||
return {"status": "success", "message": "data dropped"}
|
||
except Exception as e:
|
||
logger.error(f"Error dropping Neo4j database {self._DATABASE}: {e}")
|
||
return {"status": "error", "message": str(e)}
|