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Merge branch 'main' into graph-viewer-webui

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ArnoChen
2025-02-10 00:54:05 +08:00
parent 10a0fa1530 832a9bb6fb
commit a62f2b382b
13 changed files with 352 additions and 610 deletions
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101
lightrag/kg/json_kv_impl.py
View File

@@ -1,63 +1,13 @@
"""
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
from typing import Any
from lightrag.utils import (
logger,
load_json,
write_json,
)
from lightrag.base import (
BaseKVStorage,
)
@@ -68,25 +18,20 @@ 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 {}
self._data: dict[str, Any] = load_json(self._file_name) or {}
self._lock = asyncio.Lock()
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_id(self, id: str) -> dict[str, Any]:
return self._data.get(id, {})
async def get_by_ids(self, ids, fields=None):
if fields is None:
return [self._data.get(id, None) for id in ids]
async def get_by_ids(self, ids: list[str]) -> list[dict[str, Any]]:
return [
(
{k: v for k, v in self._data[id].items() if k in fields}
{k: v for k, v in self._data[id].items()}
if self._data.get(id, None)
else None
)
@@ -96,39 +41,9 @@ 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]):
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 filter(self, filter_func):
"""Filter key-value pairs based on a filter function
Args:
filter_func: The filter function, which takes a value as an argument and returns a boolean value
Returns:
Dict: Key-value pairs that meet the condition
"""
result = {}
async with self._lock:
for key, value in self._data.items():
if filter_func(value):
result[key] = value
return result
async def delete(self, ids: list[str]):
"""Delete data with specified IDs
Args:
ids: List of IDs to delete
"""
async with self._lock:
for id in ids:
if id in self._data:
del self._data[id]
await self.index_done_callback()
logger.info(f"Successfully deleted {len(ids)} items from {self.namespace}")

17
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
from lightrag.utils import (
logger,
@@ -72,7 +72,7 @@ class JsonDocStatusStorage(DocStatusStorage):
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 {}
self._data: dict[str, Any] = load_json(self._file_name) or {}
logger.info(f"Loaded document status storage with {len(self._data)} records")
async def filter_keys(self, data: list[str]) -> set[str]:
@@ -85,18 +85,18 @@ class JsonDocStatusStorage(DocStatusStorage):
]
)
async def get_status_counts(self) -> Dict[str, int]:
async def get_status_counts(self) -> dict[str, int]:
"""Get counts of documents in each status"""
counts = {status: 0 for status in DocStatus}
for doc in self._data.values():
counts[doc["status"]] += 1
return counts
async def get_failed_docs(self) -> Dict[str, DocProcessingStatus]:
async def get_failed_docs(self) -> dict[str, DocProcessingStatus]:
"""Get all failed documents"""
return {k: v for k, v in self._data.items() if v["status"] == DocStatus.FAILED}
async def get_pending_docs(self) -> Dict[str, DocProcessingStatus]:
async def get_pending_docs(self) -> dict[str, DocProcessingStatus]:
"""Get all pending documents"""
return {k: v for k, v in self._data.items() if v["status"] == DocStatus.PENDING}
@@ -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:
@@ -112,10 +112,9 @@ class JsonDocStatusStorage(DocStatusStorage):
"""
self._data.update(data)
await self.index_done_callback()
return data
async def get_by_id(self, id: str):
return self._data.get(id)
async def get_by_id(self, id: str) -> dict[str, Any]:
return self._data.get(id, {})
async def get(self, doc_id: str) -> Union[DocProcessingStatus, None]:
"""Get document status by ID"""

27
lightrag/kg/mongo_impl.py
View File

@@ -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, Union, List, Tuple
from ..utils import logger
from ..base import BaseKVStorage, BaseGraphStorage
@@ -29,21 +29,11 @@ class MongoKVStorage(BaseKVStorage):
self._data = database.get_collection(self.namespace)
logger.info(f"Use MongoDB as KV {self.namespace}")
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) -> dict[str, Any]:
return self._data.find_one({"_id": id})
async def get_by_ids(self, ids, fields=None):
if fields is 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 get_by_ids(self, ids: list[str]) -> list[dict[str, Any]]:
return list(self._data.find({"_id": {"$in": ids}}))
async def filter_keys(self, data: list[str]) -> set[str]:
existing_ids = [
@@ -51,7 +41,7 @@ class MongoKVStorage(BaseKVStorage):
]
return set([s for s in data if s not in existing_ids])
async def upsert(self, data: dict[str, dict]):
async def upsert(self, data: dict[str, dict[str, Any]]) -> None:
if is_namespace(self.namespace, NameSpace.KV_STORE_LLM_RESPONSE_CACHE):
for mode, items in data.items():
for k, v in tqdm_async(items.items(), desc="Upserting"):
@@ -66,7 +56,6 @@ class MongoKVStorage(BaseKVStorage):
for k, v in tqdm_async(data.items(), desc="Upserting"):
self._data.update_one({"_id": k}, {"$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 +70,9 @@ class MongoKVStorage(BaseKVStorage):
else:
return None
async def drop(self):
""" """
pass
async def drop(self) -> None:
"""Drop the collection"""
await self._data.drop()
@dataclass

46
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, 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) -> dict[str, Any]:
"""get doc_full data based on id."""
SQL = SQL_TEMPLATES["get_by_id_" + self.namespace]
params = {"workspace": self.db.workspace, "id": id}
@@ -191,12 +191,9 @@ class OracleKVStorage(BaseKVStorage):
res = {}
for row in array_res:
res[row["id"]] = row
else:
res = await self.db.query(SQL, params)
if res:
return res
else:
return None
return await self.db.query(SQL, params)
async def get_by_mode_and_id(self, mode: str, id: str) -> Union[dict, None]:
"""Specifically for llm_response_cache."""
@@ -211,7 +208,7 @@ 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[dict[str, Any]]:
"""get doc_chunks data based on id"""
SQL = SQL_TEMPLATES["get_by_ids_" + self.namespace].format(
ids=",".join([f"'{id}'" for id in ids])
@@ -230,29 +227,7 @@ class OracleKVStorage(BaseKVStorage):
for row in res:
dict_res[row["mode"]][row["id"]] = row
res = [{k: v} for k, v in dict_res.items()]
if res:
data = res # [{"data":i} for i in res]
# print(data)
return data
else:
return None
async def get_by_status_and_ids(
self, status: str, ids: list[str]
) -> Union[list[dict], 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)
if res:
return res
else:
return None
return res
async def filter_keys(self, keys: list[str]) -> set[str]:
"""Return keys that don't exist in storage"""
@@ -270,7 +245,7 @@ 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 +303,6 @@ 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(
@@ -745,7 +712,6 @@ 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)

44
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) -> dict[str, Any]:
"""Get doc_full data by id."""
sql = SQL_TEMPLATES["get_by_id_" + self.namespace]
params = {"workspace": self.db.workspace, "id": id}
@@ -193,12 +192,9 @@ class PGKVStorage(BaseKVStorage):
res = {}
for row in array_res:
res[row["id"]] = row
else:
res = await self.db.query(sql, params)
if res:
return res
else:
return None
return await self.db.query(sql, params)
async def get_by_mode_and_id(self, mode: str, id: str) -> Union[dict, None]:
"""Specifically for llm_response_cache."""
@@ -214,7 +210,7 @@ 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[dict[str, Any]]:
"""Get doc_chunks data by id"""
sql = SQL_TEMPLATES["get_by_ids_" + self.namespace].format(
ids=",".join([f"'{id}'" for id in ids])
@@ -231,23 +227,15 @@ class PGKVStorage(BaseKVStorage):
dict_res[mode] = {}
for row in array_res:
dict_res[row["mode"]][row["id"]] = row
res = [{k: v} for k, v in dict_res.items()]
return [{k: v} for k, v in dict_res.items()]
else:
res = await self.db.query(sql, params, multirows=True)
if res:
return res
else:
return None
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"
res = await self.db.query(sql, multirows=True)
return res
else:
logger.error(
f"all_keys is only implemented for llm_response_cache, not for {self.namespace}"
)
async def get_by_status(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 filter_keys(self, keys: List[str]) -> Set[str]:
"""Filter out duplicated content"""
@@ -270,7 +258,7 @@ 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):
@@ -447,14 +435,15 @@ 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) -> dict[str, Any]:
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)
if result is None or result == []:
return None
return {}
else:
return DocProcessingStatus(
content=result[0]["content"],
content_length=result[0]["content_length"],
content_summary=result[0]["content_summary"],
status=result[0]["status"],
@@ -483,10 +472,9 @@ class PGDocStatusStorage(DocStatusStorage):
sql = "select * from LIGHTRAG_DOC_STATUS where workspace=$1 and status=$1"
params = {"workspace": self.db.workspace, "status": status}
result = await self.db.query(sql, params, True)
# Result is like [{'id': 'id1', 'status': 'PENDING', 'updated_at': '2023-07-01 00:00:00'}, {'id': 'id2', 'status': 'PENDING', 'updated_at': '2023-07-01 00:00:00'}, ...]
# Converting to be a dict
return {
element["id"]: DocProcessingStatus(
content=result[0]["content"],
content_summary=element["content_summary"],
content_length=element["content_length"],
status=element["status"],
@@ -518,6 +506,7 @@ class PGDocStatusStorage(DocStatusStorage):
sql = """insert into LIGHTRAG_DOC_STATUS(workspace,id,content_summary,content_length,chunks_count,status)
values($1,$2,$3,$4,$5,$6)
on conflict(id,workspace) do update set
content = EXCLUDED.content,
content_summary = EXCLUDED.content_summary,
content_length = EXCLUDED.content_length,
chunks_count = EXCLUDED.chunks_count,
@@ -530,6 +519,7 @@ class PGDocStatusStorage(DocStatusStorage):
{
"workspace": self.db.workspace,
"id": k,
"content": v["content"],
"content_summary": v["content_summary"],
"content_length": v["content_length"],
"chunks_count": v["chunks_count"] if "chunks_count" in v else -1,

22
lightrag/kg/redis_impl.py
View File

@@ -1,4 +1,5 @@
import os
from typing import Any
from tqdm.asyncio import tqdm as tqdm_async
from dataclasses import dataclass
import pipmaster as pm
@@ -20,29 +21,15 @@ class RedisKVStorage(BaseKVStorage):
self._redis = Redis.from_url(redis_url, decode_responses=True)
logger.info(f"Use Redis as KV {self.namespace}")
async def all_keys(self) -> list[str]:
keys = await self._redis.keys(f"{self.namespace}:*")
return [key.split(":", 1)[-1] for key in keys]
async def get_by_id(self, id):
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[dict[str, Any]]:
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 +41,7 @@ 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 +49,8 @@ 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)

34
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, Union
import numpy as np
import pipmaster as pm
@@ -108,33 +108,20 @@ class TiDBKVStorage(BaseKVStorage):
################ QUERY METHODS ################
async def get_by_id(self, id: str) -> Union[dict, None]:
"""根据 id 获取 doc_full 数据."""
async def get_by_id(self, id: str) -> dict[str, Any]:
"""Fetch doc_full data by id."""
SQL = SQL_TEMPLATES["get_by_id_" + self.namespace]
params = {"id": id}
# print("get_by_id:"+SQL)
res = await self.db.query(SQL, params)
if res:
data = res # {"data":res}
# print (data)
return data
else:
return None
return await self.db.query(SQL, params)
# Query by id
async def get_by_ids(self, ids: list[str], fields=None) -> Union[list[dict], None]:
"""根据 id 获取 doc_chunks 数据"""
async def get_by_ids(self, ids: list[str]) -> list[dict[str, Any]]:
"""Fetch doc_chunks data by id"""
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
return await self.db.query(SQL, multirows=True)
async def filter_keys(self, keys: list[str]) -> set[str]:
"""过滤掉重复内容"""
@@ -158,7 +145,7 @@ 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 +322,11 @@ class TiDBVectorDBStorage(BaseVectorStorage):
merge_sql = SQL_TEMPLATES["insert_relationship"]
await self.db.execute(merge_sql, data)
async def get_by_status(self, status: str) -> Union[list[dict[str, Any]], 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):