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implemented method and cleaned the mess

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This commit is contained in:
Yannick Stephan
2025-02-08 23:18:12 +01:00
parent eb552afcdc
commit cff415d91f
7 changed files with 66 additions and 125 deletions
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63
lightrag/kg/json_kv_impl.py
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@@ -1,53 +1,3 @@
"""
JsonDocStatus Storage Module
=======================
This module provides a storage interface for graphs using NetworkX, a popular Python library for creating, manipulating, and studying the structure, dynamics, and functions of complex networks.
The `NetworkXStorage` class extends the `BaseGraphStorage` class from the LightRAG library, providing methods to load, save, manipulate, and query graphs using NetworkX.
Author: lightrag team
Created: 2024-01-25
License: MIT
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Version: 1.0.0
Dependencies:
- NetworkX
- NumPy
- LightRAG
- graspologic
Features:
- Load and save graphs in various formats (e.g., GEXF, GraphML, JSON)
- Query graph nodes and edges
- Calculate node and edge degrees
- Embed nodes using various algorithms (e.g., Node2Vec)
- Remove nodes and edges from the graph
Usage:
from lightrag.storage.networkx_storage import NetworkXStorage
"""
import asyncio
import os
from dataclasses import dataclass
@@ -58,12 +8,10 @@ from lightrag.utils import (
load_json,
write_json,
)
from lightrag.base import (
BaseKVStorage,
)
@dataclass
class JsonKVStorage(BaseKVStorage):
def __post_init__(self):
@@ -79,13 +27,13 @@ class JsonKVStorage(BaseKVStorage):
async def index_done_callback(self):
write_json(self._data, self._file_name)
async def get_by_id(self, id: str):
async def get_by_id(self, id: str) -> Union[dict[str, Any], None]:
return self._data.get(id, None)
async def get_by_ids(self, ids: list[str]):
async def get_by_ids(self, ids: list[str]) -> list[Union[dict[str, Any], None]]:
return [
(
{k: v for k, v in self._data[id].items() }
{k: v for k, v in self._data[id].items()}
if self._data.get(id, None)
else None
)
@@ -95,12 +43,11 @@ class JsonKVStorage(BaseKVStorage):
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[str, Any]]):
async def upsert(self, data: dict[str, dict[str, Any]]) -> None:
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):
async def drop(self) -> None:
self._data = {}
async def get_by_status_and_ids(

6
lightrag/kg/jsondocstatus_impl.py
View File

@@ -50,7 +50,7 @@ Usage:
import os
from dataclasses import dataclass
from typing import Union, Dict
from typing import Any, Union, Dict
from lightrag.utils import (
logger,
@@ -104,7 +104,7 @@ class JsonDocStatusStorage(DocStatusStorage):
"""Save data to file after indexing"""
write_json(self._data, self._file_name)
async def upsert(self, data: dict[str, dict]):
async def upsert(self, data: dict[str, Any]) -> None:
"""Update or insert document status
Args:
@@ -114,7 +114,7 @@ class JsonDocStatusStorage(DocStatusStorage):
await self.index_done_callback()
return data
async def get_by_id(self, id: str):
async def get_by_id(self, id: str) -> Union[dict[str, Any], None]:
return self._data.get(id)
async def get(self, doc_id: str) -> Union[DocProcessingStatus, None]:

28
lightrag/kg/mongo_impl.py
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@@ -12,7 +12,7 @@ if not pm.is_installed("motor"):
from pymongo import MongoClient
from motor.motor_asyncio import AsyncIOMotorClient
from typing import Union, List, Tuple
from typing import Any, TypeVar, Union, List, Tuple
from ..utils import logger
from ..base import BaseKVStorage, BaseGraphStorage
@@ -32,18 +32,11 @@ class MongoKVStorage(BaseKVStorage):
async def all_keys(self) -> list[str]:
return [x["_id"] for x in self._data.find({}, {"_id": 1})]
async def get_by_id(self, id):
async def get_by_id(self, id: str) -> Union[dict[str, Any], None]:
return self._data.find_one({"_id": id})
async def get_by_ids(self, ids, fields=None):
if fields is None:
async def get_by_ids(self, ids: list[str]) -> list[Union[dict[str, Any], None]]:
return list(self._data.find({"_id": {"$in": ids}}))
return list(
self._data.find(
{"_id": {"$in": ids}},
{field: 1 for field in fields},
)
)
async def filter_keys(self, data: list[str]) -> set[str]:
existing_ids = [
@@ -51,7 +44,7 @@ class MongoKVStorage(BaseKVStorage):
]
return set([s for s in data if s not in existing_ids])
async def upsert(self, data: dict[str, dict]):
async def upsert(self, data: dict[str, dict[str, Any]]) -> None:
if is_namespace(self.namespace, NameSpace.KV_STORE_LLM_RESPONSE_CACHE):
for mode, items in data.items():
for k, v in tqdm_async(items.items(), desc="Upserting"):
@@ -66,7 +59,6 @@ class MongoKVStorage(BaseKVStorage):
for k, v in tqdm_async(data.items(), desc="Upserting"):
self._data.update_one({"_id": k}, {"$set": v}, upsert=True)
data[k]["_id"] = k
return data
async def get_by_mode_and_id(self, mode: str, id: str) -> Union[dict, None]:
if is_namespace(self.namespace, NameSpace.KV_STORE_LLM_RESPONSE_CACHE):
@@ -81,9 +73,15 @@ class MongoKVStorage(BaseKVStorage):
else:
return None
async def drop(self):
""" """
pass
async def drop(self) -> None:
"""Drop the collection"""
await self._data.drop()
async def get_by_status_and_ids(
self, status: str
) -> Union[list[dict[str, Any]], None]:
"""Get documents by status and ids"""
return self._data.find({"status": status})
@dataclass

27
lightrag/kg/oracle_impl.py
View File

@@ -4,7 +4,7 @@ import asyncio
# import html
# import os
from dataclasses import dataclass
from typing import Union
from typing import Any, TypeVar, Union
import numpy as np
import array
import pipmaster as pm
@@ -181,7 +181,7 @@ class OracleKVStorage(BaseKVStorage):
################ QUERY METHODS ################
async def get_by_id(self, id: str) -> Union[dict, None]:
async def get_by_id(self, id: str) -> Union[dict[str, Any], None]:
"""get doc_full data based on id."""
SQL = SQL_TEMPLATES["get_by_id_" + self.namespace]
params = {"workspace": self.db.workspace, "id": id}
@@ -211,7 +211,7 @@ class OracleKVStorage(BaseKVStorage):
else:
return None
async def get_by_ids(self, ids: list[str], fields=None) -> Union[list[dict], None]:
async def get_by_ids(self, ids: list[str]) -> list[Union[dict[str, Any], None]]:
"""get doc_chunks data based on id"""
SQL = SQL_TEMPLATES["get_by_ids_" + self.namespace].format(
ids=",".join([f"'{id}'" for id in ids])
@@ -238,14 +238,9 @@ class OracleKVStorage(BaseKVStorage):
return None
async def get_by_status_and_ids(
self, status: str, ids: list[str]
) -> Union[list[dict], None]:
self, status: str
) -> Union[list[dict[str, Any]], None]:
"""Specifically for llm_response_cache."""
if ids is not None:
SQL = SQL_TEMPLATES["get_by_status_ids_" + self.namespace].format(
ids=",".join([f"'{id}'" for id in ids])
)
else:
SQL = SQL_TEMPLATES["get_by_status_" + self.namespace]
params = {"workspace": self.db.workspace, "status": status}
res = await self.db.query(SQL, params, multirows=True)
@@ -270,7 +265,7 @@ class OracleKVStorage(BaseKVStorage):
return set(keys)
################ INSERT METHODS ################
async def upsert(self, data: dict[str, dict]):
async def upsert(self, data: dict[str, Any]) -> None:
if is_namespace(self.namespace, NameSpace.KV_STORE_TEXT_CHUNKS):
list_data = [
{
@@ -328,14 +323,6 @@ class OracleKVStorage(BaseKVStorage):
}
await self.db.execute(upsert_sql, _data)
return None
async def change_status(self, id: str, status: str):
SQL = SQL_TEMPLATES["change_status"].format(
table_name=namespace_to_table_name(self.namespace)
)
params = {"workspace": self.db.workspace, "id": id, "status": status}
await self.db.execute(SQL, params)
async def index_done_callback(self):
if is_namespace(
@@ -344,7 +331,6 @@ class OracleKVStorage(BaseKVStorage):
):
logger.info("full doc and chunk data had been saved into oracle db!")
@dataclass
class OracleVectorDBStorage(BaseVectorStorage):
# should pass db object to self.db
@@ -745,7 +731,6 @@ SQL_TEMPLATES = {
"get_by_status_full_docs": "select id,status from LIGHTRAG_DOC_FULL t where workspace=:workspace AND status=:status",
"get_by_status_text_chunks": "select id,status from LIGHTRAG_DOC_CHUNKS where workspace=:workspace and status=:status",
"filter_keys": "select id from {table_name} where workspace=:workspace and id in ({ids})",
"change_status": "update {table_name} set status=:status,updatetime=SYSDATE where workspace=:workspace and id=:id",
"merge_doc_full": """MERGE INTO LIGHTRAG_DOC_FULL a
USING DUAL
ON (a.id = :id and a.workspace = :workspace)

17
lightrag/kg/postgres_impl.py
View File

@@ -30,7 +30,6 @@ from ..base import (
DocStatus,
DocProcessingStatus,
BaseGraphStorage,
T,
)
from ..namespace import NameSpace, is_namespace
@@ -184,7 +183,7 @@ class PGKVStorage(BaseKVStorage):
################ QUERY METHODS ################
async def get_by_id(self, id: str) -> Union[dict, None]:
async def get_by_id(self, id: str) -> Union[dict[str, Any], None]:
"""Get doc_full data by id."""
sql = SQL_TEMPLATES["get_by_id_" + self.namespace]
params = {"workspace": self.db.workspace, "id": id}
@@ -214,7 +213,7 @@ class PGKVStorage(BaseKVStorage):
return None
# Query by id
async def get_by_ids(self, ids: List[str], fields=None) -> Union[List[dict], None]:
async def get_by_ids(self, ids: list[str]) -> list[Union[dict[str, Any], None]]:
"""Get doc_chunks data by id"""
sql = SQL_TEMPLATES["get_by_ids_" + self.namespace].format(
ids=",".join([f"'{id}'" for id in ids])
@@ -239,6 +238,14 @@ class PGKVStorage(BaseKVStorage):
else:
return None
async def get_by_status_and_ids(
self, status: str
) -> Union[list[dict[str, Any]], None]:
"""Specifically for llm_response_cache."""
SQL = SQL_TEMPLATES["get_by_status_" + self.namespace]
params = {"workspace": self.db.workspace, "status": status}
return await self.db.query(SQL, params, multirows=True)
async def all_keys(self) -> list[dict]:
if is_namespace(self.namespace, NameSpace.KV_STORE_LLM_RESPONSE_CACHE):
sql = "select workspace,mode,id from lightrag_llm_cache"
@@ -270,7 +277,7 @@ class PGKVStorage(BaseKVStorage):
print(params)
################ INSERT METHODS ################
async def upsert(self, data: Dict[str, dict]):
async def upsert(self, data: dict[str, Any]) -> None:
if is_namespace(self.namespace, NameSpace.KV_STORE_TEXT_CHUNKS):
pass
elif is_namespace(self.namespace, NameSpace.KV_STORE_FULL_DOCS):
@@ -447,7 +454,7 @@ class PGDocStatusStorage(DocStatusStorage):
existed = set([element["id"] for element in result])
return set(data) - existed
async def get_by_id(self, id: str) -> Union[T, None]:
async def get_by_id(self, id: str) -> Union[dict[str, Any], None]:
sql = "select * from LIGHTRAG_DOC_STATUS where workspace=$1 and id=$2"
params = {"workspace": self.db.workspace, "id": id}
result = await self.db.query(sql, params, True)

28
lightrag/kg/redis_impl.py
View File

@@ -1,4 +1,5 @@
import os
from typing import Any, TypeVar, Union
from tqdm.asyncio import tqdm as tqdm_async
from dataclasses import dataclass
import pipmaster as pm
@@ -28,21 +29,11 @@ class RedisKVStorage(BaseKVStorage):
data = await self._redis.get(f"{self.namespace}:{id}")
return json.loads(data) if data else None
async def get_by_ids(self, ids, fields=None):
async def get_by_ids(self, ids: list[str]) -> list[Union[dict[str, Any], None]]:
pipe = self._redis.pipeline()
for id in ids:
pipe.get(f"{self.namespace}:{id}")
results = await pipe.execute()
if fields:
# Filter fields if specified
return [
{field: value.get(field) for field in fields if field in value}
if (value := json.loads(result))
else None
for result in results
]
return [json.loads(result) if result else None for result in results]
async def filter_keys(self, data: list[str]) -> set[str]:
@@ -54,7 +45,7 @@ class RedisKVStorage(BaseKVStorage):
existing_ids = {data[i] for i, exists in enumerate(results) if exists}
return set(data) - existing_ids
async def upsert(self, data: dict[str, dict]):
async def upsert(self, data: dict[str, Any]) -> None:
pipe = self._redis.pipeline()
for k, v in tqdm_async(data.items(), desc="Upserting"):
pipe.set(f"{self.namespace}:{k}", json.dumps(v))
@@ -62,9 +53,18 @@ class RedisKVStorage(BaseKVStorage):
for k in data:
data[k]["_id"] = k
return data
async def drop(self):
async def drop(self) -> None:
keys = await self._redis.keys(f"{self.namespace}:*")
if keys:
await self._redis.delete(*keys)
async def get_by_status_and_ids(
self, status: str,
) -> Union[list[dict[str, Any]], None]:
pipe = self._redis.pipeline()
for key in await self._redis.keys(f"{self.namespace}:*"):
pipe.hgetall(key)
results = await pipe.execute()
return [data for data in results if data.get("status") == status] or None

16
lightrag/kg/tidb_impl.py
View File

@@ -1,7 +1,7 @@
import asyncio
import os
from dataclasses import dataclass
from typing import Union
from typing import Any, TypeVar, Union
import numpy as np
import pipmaster as pm
@@ -108,7 +108,7 @@ class TiDBKVStorage(BaseKVStorage):
################ QUERY METHODS ################
async def get_by_id(self, id: str) -> Union[dict, None]:
async def get_by_id(self, id: str) -> Union[dict[str, Any], None]:
"""根据 id 获取 doc_full 数据."""
SQL = SQL_TEMPLATES["get_by_id_" + self.namespace]
params = {"id": id}
@@ -122,16 +122,14 @@ class TiDBKVStorage(BaseKVStorage):
return None
# Query by id
async def get_by_ids(self, ids: list[str], fields=None) -> Union[list[dict], None]:
async def get_by_ids(self, ids: list[str]) -> list[Union[dict[str, Any], None]]:
"""根据 id 获取 doc_chunks 数据"""
SQL = SQL_TEMPLATES["get_by_ids_" + self.namespace].format(
ids=",".join([f"'{id}'" for id in ids])
)
# print("get_by_ids:"+SQL)
res = await self.db.query(SQL, multirows=True)
if res:
data = res # [{"data":i} for i in res]
# print(data)
return data
else:
return None
@@ -158,7 +156,7 @@ class TiDBKVStorage(BaseKVStorage):
return data
################ INSERT full_doc AND chunks ################
async def upsert(self, data: dict[str, dict]):
async def upsert(self, data: dict[str, Any]) -> None:
left_data = {k: v for k, v in data.items() if k not in self._data}
self._data.update(left_data)
if is_namespace(self.namespace, NameSpace.KV_STORE_TEXT_CHUNKS):
@@ -335,6 +333,12 @@ class TiDBVectorDBStorage(BaseVectorStorage):
merge_sql = SQL_TEMPLATES["insert_relationship"]
await self.db.execute(merge_sql, data)
async def get_by_status_and_ids(
self, status: str
) -> Union[list[dict], None]:
SQL = SQL_TEMPLATES["get_by_status_" + self.namespace]
params = {"workspace": self.db.workspace, "status": status}
return await self.db.query(SQL, params, multirows=True)
@dataclass
class TiDBGraphStorage(BaseGraphStorage):