Refactor graphrag to remove redis lock (#5828)

### What problem does this PR solve?

Refactor graphrag to remove redis lock

### Type of change

- [x] Refactoring
This commit is contained in:
Zhichang Yu
2025-03-10 15:15:06 +08:00
committed by GitHub
parent 1163e9e409
commit 6ec6ca6971
9 changed files with 602 additions and 332 deletions

View File

@ -93,7 +93,7 @@ class Extractor:
return dict(maybe_nodes), dict(maybe_edges)
async def __call__(
self, chunks: list[tuple[str, str]],
self, doc_id: str, chunks: list[str],
callback: Callable | None = None
):
@ -101,9 +101,9 @@ class Extractor:
start_ts = trio.current_time()
out_results = []
async with trio.open_nursery() as nursery:
for i, (cid, ck) in enumerate(chunks):
for i, ck in enumerate(chunks):
ck = truncate(ck, int(self._llm.max_length*0.8))
nursery.start_soon(lambda: self._process_single_content((cid, ck), i, len(chunks), out_results))
nursery.start_soon(lambda: self._process_single_content((doc_id, ck), i, len(chunks), out_results))
maybe_nodes = defaultdict(list)
maybe_edges = defaultdict(list)
@ -241,10 +241,13 @@ class Extractor:
) -> str:
summary_max_tokens = 512
use_description = truncate(description, summary_max_tokens)
description_list=use_description.split(GRAPH_FIELD_SEP),
if len(description_list) <= 12:
return use_description
prompt_template = SUMMARIZE_DESCRIPTIONS_PROMPT
context_base = dict(
entity_name=entity_or_relation_name,
description_list=use_description.split(GRAPH_FIELD_SEP),
description_list=description_list,
language=self._language,
)
use_prompt = prompt_template.format(**context_base)

View File

@ -15,196 +15,353 @@
#
import json
import logging
from functools import reduce, partial
from functools import partial
import networkx as nx
import trio
from api import settings
from graphrag.light.graph_extractor import GraphExtractor as LightKGExt
from graphrag.general.graph_extractor import GraphExtractor as GeneralKGExt
from graphrag.general.community_reports_extractor import CommunityReportsExtractor
from graphrag.entity_resolution import EntityResolution
from graphrag.general.extractor import Extractor
from graphrag.general.graph_extractor import DEFAULT_ENTITY_TYPES
from graphrag.utils import graph_merge, set_entity, get_relation, set_relation, get_entity, get_graph, set_graph, \
chunk_id, update_nodes_pagerank_nhop_neighbour
from graphrag.utils import (
graph_merge,
set_entity,
get_relation,
set_relation,
get_entity,
get_graph,
set_graph,
chunk_id,
update_nodes_pagerank_nhop_neighbour,
does_graph_contains,
get_graph_doc_ids,
)
from rag.nlp import rag_tokenizer, search
from rag.utils.redis_conn import RedisDistributedLock
from rag.utils.redis_conn import REDIS_CONN
class Dealer:
def __init__(self,
extractor: Extractor,
tenant_id: str,
kb_id: str,
llm_bdl,
chunks: list[tuple[str, str]],
language,
entity_types=DEFAULT_ENTITY_TYPES,
embed_bdl=None,
callback=None
):
self.tenant_id = tenant_id
self.kb_id = kb_id
self.chunks = chunks
self.llm_bdl = llm_bdl
self.embed_bdl = embed_bdl
self.ext = extractor(self.llm_bdl, language=language,
entity_types=entity_types,
get_entity=partial(get_entity, tenant_id, kb_id),
set_entity=partial(set_entity, tenant_id, kb_id, self.embed_bdl),
get_relation=partial(get_relation, tenant_id, kb_id),
set_relation=partial(set_relation, tenant_id, kb_id, self.embed_bdl)
)
self.graph = nx.Graph()
self.callback = callback
def graphrag_task_set(tenant_id, kb_id, doc_id) -> bool:
key = f"graphrag:{tenant_id}:{kb_id}"
ok = REDIS_CONN.set(key, doc_id, exp=3600 * 24)
if not ok:
raise Exception(f"Faild to set the {key} to {doc_id}")
async def __call__(self):
docids = list(set([docid for docid, _ in self.chunks]))
ents, rels = await self.ext(self.chunks, self.callback)
for en in ents:
self.graph.add_node(en["entity_name"], entity_type=en["entity_type"])#, description=en["description"])
for rel in rels:
self.graph.add_edge(
rel["src_id"],
rel["tgt_id"],
weight=rel["weight"],
#description=rel["description"]
def graphrag_task_get(tenant_id, kb_id) -> str | None:
key = f"graphrag:{tenant_id}:{kb_id}"
doc_id = REDIS_CONN.get(key)
return doc_id
async def run_graphrag(
row: dict,
language,
with_resolution: bool,
with_community: bool,
chat_model,
embedding_model,
callback,
):
start = trio.current_time()
tenant_id, kb_id, doc_id = row["tenant_id"], str(row["kb_id"]), row["doc_id"]
chunks = []
for d in settings.retrievaler.chunk_list(
doc_id, tenant_id, [kb_id], fields=["content_with_weight", "doc_id"]
):
chunks.append(d["content_with_weight"])
graph, doc_ids = await update_graph(
LightKGExt
if row["parser_config"]["graphrag"]["method"] != "general"
else GeneralKGExt,
tenant_id,
kb_id,
doc_id,
chunks,
language,
row["parser_config"]["graphrag"]["entity_types"],
chat_model,
embedding_model,
callback,
)
if not graph:
return
if with_resolution or with_community:
graphrag_task_set(tenant_id, kb_id, doc_id)
if with_resolution:
await resolve_entities(
graph,
doc_ids,
tenant_id,
kb_id,
doc_id,
chat_model,
embedding_model,
callback,
)
if with_community:
await extract_community(
graph,
doc_ids,
tenant_id,
kb_id,
doc_id,
chat_model,
embedding_model,
callback,
)
now = trio.current_time()
callback(msg=f"GraphRAG for doc {doc_id} done in {now - start:.2f} seconds.")
return
async def update_graph(
extractor: Extractor,
tenant_id: str,
kb_id: str,
doc_id: str,
chunks: list[str],
language,
entity_types,
llm_bdl,
embed_bdl,
callback,
):
contains = await does_graph_contains(tenant_id, kb_id, doc_id)
if contains:
callback(msg=f"Graph already contains {doc_id}, cancel myself")
return None, None
start = trio.current_time()
ext = extractor(
llm_bdl,
language=language,
entity_types=entity_types,
get_entity=partial(get_entity, tenant_id, kb_id),
set_entity=partial(set_entity, tenant_id, kb_id, embed_bdl),
get_relation=partial(get_relation, tenant_id, kb_id),
set_relation=partial(set_relation, tenant_id, kb_id, embed_bdl),
)
ents, rels = await ext(doc_id, chunks, callback)
subgraph = nx.Graph()
for en in ents:
subgraph.add_node(en["entity_name"], entity_type=en["entity_type"])
for rel in rels:
subgraph.add_edge(
rel["src_id"],
rel["tgt_id"],
weight=rel["weight"],
# description=rel["description"]
)
# TODO: infinity doesn't support array search
chunk = {
"content_with_weight": json.dumps(
nx.node_link_data(subgraph, edges="edges"), ensure_ascii=False, indent=2
),
"knowledge_graph_kwd": "subgraph",
"kb_id": kb_id,
"source_id": [doc_id],
"available_int": 0,
"removed_kwd": "N",
}
cid = chunk_id(chunk)
await trio.to_thread.run_sync(
lambda: settings.docStoreConn.insert(
[{"id": cid, **chunk}], search.index_name(tenant_id), kb_id
)
)
now = trio.current_time()
callback(msg=f"generated subgraph for doc {doc_id} in {now - start:.2f} seconds.")
start = now
while True:
new_graph = subgraph
now_docids = set([doc_id])
old_graph, old_doc_ids = await get_graph(tenant_id, kb_id)
if old_graph is not None:
logging.info("Merge with an exiting graph...................")
new_graph = graph_merge(old_graph, subgraph)
await update_nodes_pagerank_nhop_neighbour(tenant_id, kb_id, new_graph, 2)
if old_doc_ids:
for old_doc_id in old_doc_ids:
now_docids.add(old_doc_id)
old_doc_ids2 = await get_graph_doc_ids(tenant_id, kb_id)
delta_doc_ids = set(old_doc_ids2) - set(old_doc_ids)
if delta_doc_ids:
callback(
msg="The global graph has changed during merging, try again"
)
with RedisDistributedLock(self.kb_id, 60*60):
old_graph, old_doc_ids = get_graph(self.tenant_id, self.kb_id)
if old_graph is not None:
logging.info("Merge with an exiting graph...................")
self.graph = reduce(graph_merge, [old_graph, self.graph])
update_nodes_pagerank_nhop_neighbour(self.tenant_id, self.kb_id, self.graph, 2)
if old_doc_ids:
docids.extend(old_doc_ids)
docids = list(set(docids))
set_graph(self.tenant_id, self.kb_id, self.graph, docids)
await trio.sleep(1)
continue
break
await set_graph(tenant_id, kb_id, new_graph, list(now_docids))
now = trio.current_time()
callback(
msg=f"merging subgraph for doc {doc_id} into the global graph done in {now - start:.2f} seconds."
)
return new_graph, now_docids
class WithResolution(Dealer):
def __init__(self,
tenant_id: str,
kb_id: str,
llm_bdl,
embed_bdl=None,
callback=None
):
self.tenant_id = tenant_id
self.kb_id = kb_id
self.llm_bdl = llm_bdl
self.embed_bdl = embed_bdl
self.callback = callback
async def __call__(self):
with RedisDistributedLock(self.kb_id, 60*60):
self.graph, doc_ids = await trio.to_thread.run_sync(lambda: get_graph(self.tenant_id, self.kb_id))
if not self.graph:
logging.error(f"Faild to fetch the graph. tenant_id:{self.kb_id}, kb_id:{self.kb_id}")
if self.callback:
self.callback(-1, msg="Faild to fetch the graph.")
return
async def resolve_entities(
graph,
doc_ids,
tenant_id: str,
kb_id: str,
doc_id: str,
llm_bdl,
embed_bdl,
callback,
):
working_doc_id = graphrag_task_get(tenant_id, kb_id)
if doc_id != working_doc_id:
callback(
msg=f"Another graphrag task of doc_id {working_doc_id} is working on this kb, cancel myself"
)
return
start = trio.current_time()
er = EntityResolution(
llm_bdl,
get_entity=partial(get_entity, tenant_id, kb_id),
set_entity=partial(set_entity, tenant_id, kb_id, embed_bdl),
get_relation=partial(get_relation, tenant_id, kb_id),
set_relation=partial(set_relation, tenant_id, kb_id, embed_bdl),
)
reso = await er(graph)
graph = reso.graph
callback(msg=f"Graph resolution removed {len(reso.removed_entities)} nodes.")
await update_nodes_pagerank_nhop_neighbour(tenant_id, kb_id, graph, 2)
callback(msg="Graph resolution updated pagerank.")
if self.callback:
self.callback(msg="Fetch the existing graph.")
er = EntityResolution(self.llm_bdl,
get_entity=partial(get_entity, self.tenant_id, self.kb_id),
set_entity=partial(set_entity, self.tenant_id, self.kb_id, self.embed_bdl),
get_relation=partial(get_relation, self.tenant_id, self.kb_id),
set_relation=partial(set_relation, self.tenant_id, self.kb_id, self.embed_bdl))
reso = await er(self.graph)
self.graph = reso.graph
logging.info("Graph resolution is done. Remove {} nodes.".format(len(reso.removed_entities)))
if self.callback:
self.callback(msg="Graph resolution is done. Remove {} nodes.".format(len(reso.removed_entities)))
await trio.to_thread.run_sync(lambda: update_nodes_pagerank_nhop_neighbour(self.tenant_id, self.kb_id, self.graph, 2))
await trio.to_thread.run_sync(lambda: set_graph(self.tenant_id, self.kb_id, self.graph, doc_ids))
working_doc_id = graphrag_task_get(tenant_id, kb_id)
if doc_id != working_doc_id:
callback(
msg=f"Another graphrag task of doc_id {working_doc_id} is working on this kb, cancel myself"
)
return
await set_graph(tenant_id, kb_id, graph, doc_ids)
await trio.to_thread.run_sync(lambda: settings.docStoreConn.delete({
"knowledge_graph_kwd": "relation",
"kb_id": self.kb_id,
"from_entity_kwd": reso.removed_entities
}, search.index_name(self.tenant_id), self.kb_id))
await trio.to_thread.run_sync(lambda: settings.docStoreConn.delete({
"knowledge_graph_kwd": "relation",
"kb_id": self.kb_id,
"to_entity_kwd": reso.removed_entities
}, search.index_name(self.tenant_id), self.kb_id))
await trio.to_thread.run_sync(lambda: settings.docStoreConn.delete({
"knowledge_graph_kwd": "entity",
"kb_id": self.kb_id,
"entity_kwd": reso.removed_entities
}, search.index_name(self.tenant_id), self.kb_id))
await trio.to_thread.run_sync(
lambda: settings.docStoreConn.delete(
{
"knowledge_graph_kwd": "relation",
"kb_id": kb_id,
"from_entity_kwd": reso.removed_entities,
},
search.index_name(tenant_id),
kb_id,
)
)
await trio.to_thread.run_sync(
lambda: settings.docStoreConn.delete(
{
"knowledge_graph_kwd": "relation",
"kb_id": kb_id,
"to_entity_kwd": reso.removed_entities,
},
search.index_name(tenant_id),
kb_id,
)
)
await trio.to_thread.run_sync(
lambda: settings.docStoreConn.delete(
{
"knowledge_graph_kwd": "entity",
"kb_id": kb_id,
"entity_kwd": reso.removed_entities,
},
search.index_name(tenant_id),
kb_id,
)
)
now = trio.current_time()
callback(msg=f"Graph resolution done in {now - start:.2f}s.")
class WithCommunity(Dealer):
def __init__(self,
tenant_id: str,
kb_id: str,
llm_bdl,
embed_bdl=None,
callback=None
):
async def extract_community(
graph,
doc_ids,
tenant_id: str,
kb_id: str,
doc_id: str,
llm_bdl,
embed_bdl,
callback,
):
working_doc_id = graphrag_task_get(tenant_id, kb_id)
if doc_id != working_doc_id:
callback(
msg=f"Another graphrag task of doc_id {working_doc_id} is working on this kb, cancel myself"
)
return
start = trio.current_time()
ext = CommunityReportsExtractor(
llm_bdl,
get_entity=partial(get_entity, tenant_id, kb_id),
set_entity=partial(set_entity, tenant_id, kb_id, embed_bdl),
get_relation=partial(get_relation, tenant_id, kb_id),
set_relation=partial(set_relation, tenant_id, kb_id, embed_bdl),
)
cr = await ext(graph, callback=callback)
community_structure = cr.structured_output
community_reports = cr.output
working_doc_id = graphrag_task_get(tenant_id, kb_id)
if doc_id != working_doc_id:
callback(
msg=f"Another graphrag task of doc_id {working_doc_id} is working on this kb, cancel myself"
)
return
await set_graph(tenant_id, kb_id, graph, doc_ids)
self.tenant_id = tenant_id
self.kb_id = kb_id
self.community_structure = None
self.community_reports = None
self.llm_bdl = llm_bdl
self.embed_bdl = embed_bdl
self.callback = callback
async def __call__(self):
with RedisDistributedLock(self.kb_id, 60*60):
self.graph, doc_ids = get_graph(self.tenant_id, self.kb_id)
if not self.graph:
logging.error(f"Faild to fetch the graph. tenant_id:{self.kb_id}, kb_id:{self.kb_id}")
if self.callback:
self.callback(-1, msg="Faild to fetch the graph.")
return
if self.callback:
self.callback(msg="Fetch the existing graph.")
cr = CommunityReportsExtractor(self.llm_bdl,
get_entity=partial(get_entity, self.tenant_id, self.kb_id),
set_entity=partial(set_entity, self.tenant_id, self.kb_id, self.embed_bdl),
get_relation=partial(get_relation, self.tenant_id, self.kb_id),
set_relation=partial(set_relation, self.tenant_id, self.kb_id, self.embed_bdl))
cr = await cr(self.graph, callback=self.callback)
self.community_structure = cr.structured_output
self.community_reports = cr.output
await trio.to_thread.run_sync(lambda: set_graph(self.tenant_id, self.kb_id, self.graph, doc_ids))
if self.callback:
self.callback(msg="Graph community extraction is done. Indexing {} reports.".format(len(cr.structured_output)))
await trio.to_thread.run_sync(lambda: settings.docStoreConn.delete({
now = trio.current_time()
callback(
msg=f"Graph extracted {len(cr.structured_output)} communities in {now - start:.2f}s."
)
start = now
await trio.to_thread.run_sync(
lambda: settings.docStoreConn.delete(
{"knowledge_graph_kwd": "community_report", "kb_id": kb_id},
search.index_name(tenant_id),
kb_id,
)
)
for stru, rep in zip(community_structure, community_reports):
obj = {
"report": rep,
"evidences": "\n".join([f["explanation"] for f in stru["findings"]]),
}
chunk = {
"docnm_kwd": stru["title"],
"title_tks": rag_tokenizer.tokenize(stru["title"]),
"content_with_weight": json.dumps(obj, ensure_ascii=False),
"content_ltks": rag_tokenizer.tokenize(
obj["report"] + " " + obj["evidences"]
),
"knowledge_graph_kwd": "community_report",
"kb_id": self.kb_id
}, search.index_name(self.tenant_id), self.kb_id))
for stru, rep in zip(self.community_structure, self.community_reports):
obj = {
"report": rep,
"evidences": "\n".join([f["explanation"] for f in stru["findings"]])
}
chunk = {
"docnm_kwd": stru["title"],
"title_tks": rag_tokenizer.tokenize(stru["title"]),
"content_with_weight": json.dumps(obj, ensure_ascii=False),
"content_ltks": rag_tokenizer.tokenize(obj["report"] +" "+ obj["evidences"]),
"knowledge_graph_kwd": "community_report",
"weight_flt": stru["weight"],
"entities_kwd": stru["entities"],
"important_kwd": stru["entities"],
"kb_id": self.kb_id,
"source_id": doc_ids,
"available_int": 0
}
chunk["content_sm_ltks"] = rag_tokenizer.fine_grained_tokenize(chunk["content_ltks"])
#try:
# ebd, _ = self.embed_bdl.encode([", ".join(community["entities"])])
# chunk["q_%d_vec" % len(ebd[0])] = ebd[0]
#except Exception as e:
# logging.exception(f"Fail to embed entity relation: {e}")
await trio.to_thread.run_sync(lambda: settings.docStoreConn.insert([{"id": chunk_id(chunk), **chunk}], search.index_name(self.tenant_id)))
"weight_flt": stru["weight"],
"entities_kwd": stru["entities"],
"important_kwd": stru["entities"],
"kb_id": kb_id,
"source_id": doc_ids,
"available_int": 0,
}
chunk["content_sm_ltks"] = rag_tokenizer.fine_grained_tokenize(
chunk["content_ltks"]
)
# try:
# ebd, _ = embed_bdl.encode([", ".join(community["entities"])])
# chunk["q_%d_vec" % len(ebd[0])] = ebd[0]
# except Exception as e:
# logging.exception(f"Fail to embed entity relation: {e}")
await trio.to_thread.run_sync(
lambda: settings.docStoreConn.insert(
[{"id": chunk_id(chunk), **chunk}], search.index_name(tenant_id)
)
)
now = trio.current_time()
callback(
msg=f"Graph indexed {len(cr.structured_output)} communities in {now - start:.2f}s."
)
return community_structure, community_reports

View File

@ -16,7 +16,7 @@
import argparse
import json
import logging
import networkx as nx
import trio
@ -26,42 +26,85 @@ from api.db.services.document_service import DocumentService
from api.db.services.knowledgebase_service import KnowledgebaseService
from api.db.services.llm_service import LLMBundle
from api.db.services.user_service import TenantService
from graphrag.general.index import WithCommunity, Dealer, WithResolution
from graphrag.light.graph_extractor import GraphExtractor
from rag.utils.redis_conn import RedisDistributedLock
from graphrag.general.graph_extractor import GraphExtractor
from graphrag.general.index import update_graph, with_resolution, with_community
settings.init_settings()
if __name__ == "__main__":
def callback(prog=None, msg="Processing..."):
logging.info(msg)
async def main():
parser = argparse.ArgumentParser()
parser.add_argument('-t', '--tenant_id', default=False, help="Tenant ID", action='store', required=True)
parser.add_argument('-d', '--doc_id', default=False, help="Document ID", action='store', required=True)
parser.add_argument(
"-t",
"--tenant_id",
default=False,
help="Tenant ID",
action="store",
required=True,
)
parser.add_argument(
"-d",
"--doc_id",
default=False,
help="Document ID",
action="store",
required=True,
)
args = parser.parse_args()
e, doc = DocumentService.get_by_id(args.doc_id)
if not e:
raise LookupError("Document not found.")
kb_id = doc.kb_id
chunks = [d["content_with_weight"] for d in
settings.retrievaler.chunk_list(args.doc_id, args.tenant_id, [kb_id], max_count=6,
fields=["content_with_weight"])]
chunks = [("x", c) for c in chunks]
RedisDistributedLock.clean_lock(kb_id)
chunks = [
d["content_with_weight"]
for d in settings.retrievaler.chunk_list(
args.doc_id,
args.tenant_id,
[kb_id],
max_count=6,
fields=["content_with_weight"],
)
]
_, tenant = TenantService.get_by_id(args.tenant_id)
llm_bdl = LLMBundle(args.tenant_id, LLMType.CHAT, tenant.llm_id)
_, kb = KnowledgebaseService.get_by_id(kb_id)
embed_bdl = LLMBundle(args.tenant_id, LLMType.EMBEDDING, kb.embd_id)
dealer = Dealer(GraphExtractor, args.tenant_id, kb_id, llm_bdl, chunks, "English", embed_bdl=embed_bdl)
trio.run(dealer())
print(json.dumps(nx.node_link_data(dealer.graph), ensure_ascii=False, indent=2))
graph, doc_ids = await update_graph(
GraphExtractor,
args.tenant_id,
kb_id,
args.doc_id,
chunks,
"English",
llm_bdl,
embed_bdl,
callback,
)
print(json.dumps(nx.node_link_data(graph), ensure_ascii=False, indent=2))
dealer = WithResolution(args.tenant_id, kb_id, llm_bdl, embed_bdl)
trio.run(dealer())
dealer = WithCommunity(args.tenant_id, kb_id, llm_bdl, embed_bdl)
trio.run(dealer())
await with_resolution(
args.tenant_id, kb_id, args.doc_id, llm_bdl, embed_bdl, callback
)
community_structure, community_reports = await with_community(
args.tenant_id, kb_id, args.doc_id, llm_bdl, embed_bdl, callback
)
print("------------------ COMMUNITY REPORT ----------------------\n", dealer.community_reports)
print(json.dumps(dealer.community_structure, ensure_ascii=False, indent=2))
print(
"------------------ COMMUNITY STRUCTURE--------------------\n",
json.dumps(community_structure, ensure_ascii=False, indent=2),
)
print(
"------------------ COMMUNITY REPORTS----------------------\n",
community_reports,
)
if __name__ == "__main__":
trio.run(main)