Feature/rework kg core (#171)

* Knowledge cores with msgpack
* Put it in the cli package
* Tidy up msgpack dumper
* Created a loader
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cybermaggedon 2024-11-25 20:46:35 +00:00 committed by GitHub
parent 319f9ac04a
commit 340d7a224f
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6 changed files with 700 additions and 4 deletions

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@ -23,3 +23,6 @@ if "error" in resp:
print(f"Error: {resp['error']}")
sys.exit(1)
print(resp["vectors"])

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@ -0,0 +1,34 @@
#!/usr/bin/env python3
import msgpack
import sys
import argparse
def run(input_file):
with open(input_file, 'rb') as f:
unpacker = msgpack.Unpacker(f, raw=False)
for unpacked in unpacker:
print(unpacked)
def main():
parser = argparse.ArgumentParser(
prog='tg-load-pdf',
description=__doc__,
)
parser.add_argument(
'-i', '--input-file',
required=True,
help=f'Input file'
)
args = parser.parse_args()
run(**vars(args))
main()

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@ -0,0 +1,179 @@
#!/usr/bin/env python3
import aiohttp
import asyncio
import msgpack
import json
import sys
import argparse
import os
async def load_ge(queue, url):
async with aiohttp.ClientSession() as session:
async with session.ws_connect(f"{url}load/graph-embeddings") as ws:
while True:
msg = await queue.get()
msg = {
"metadata": {
"id": msg["m"]["i"],
"metadata": msg["m"]["m"],
"user": msg["m"]["u"],
"collection": msg["m"]["c"],
},
"vectors": msg["v"],
"entity": msg["e"],
}
await ws.send_json(msg)
async def load_triples(queue, url):
async with aiohttp.ClientSession() as session:
async with session.ws_connect(f"{url}load/triples") as ws:
while True:
msg = await queue.get()
msg ={
"metadata": {
"id": msg["m"]["i"],
"metadata": msg["m"]["m"],
"user": msg["m"]["u"],
"collection": msg["m"]["c"],
},
"triples": msg["t"],
}
await ws.send_json(msg)
ge_counts = 0
t_counts = 0
async def stats():
global t_counts
global ge_counts
while True:
await asyncio.sleep(5)
print(
f"Graph embeddings: {ge_counts:10d} Triples: {t_counts:10d}"
)
async def loader(ge_queue, t_queue, path, format, user, collection):
global t_counts
global ge_counts
if format == "json":
raise RuntimeError("Not implemented")
else:
with open(path, "rb") as f:
unpacker = msgpack.Unpacker(f, raw=False)
for unpacked in unpacker:
if user:
unpacked["metadata"]["user"] = user
if collection:
unpacked["metadata"]["collection"] = collection
if unpacked[0] == "t":
await t_queue.put(unpacked[1])
t_counts += 1
else:
if unpacked[0] == "ge":
await ge_queue.put(unpacked[1])
ge_counts += 1
async def run(**args):
ge_q = asyncio.Queue()
t_q = asyncio.Queue()
load_task = asyncio.create_task(
loader(
ge_queue=ge_q, t_queue=t_q,
path=args["input_file"], format=args["format"],
user=args["user"], collection=args["collection"],
)
)
ge_task = asyncio.create_task(
load_ge(
queue=ge_q, url=args["url"] + "api/v1/"
)
)
triples_task = asyncio.create_task(
load_triples(
queue=t_q, url=args["url"] + "api/v1/"
)
)
stats_task = asyncio.create_task(stats())
await load_task
await triples_task
await ge_task
await stats_task
async def main():
parser = argparse.ArgumentParser(
prog='tg-load-pdf',
description=__doc__,
)
default_url = os.getenv("TRUSTGRAPH_API", "http://localhost:8088/")
default_user = "trustgraph"
collection = "default"
parser.add_argument(
'-u', '--url',
default=default_url,
help=f'TrustGraph API URL (default: {default_url})',
)
parser.add_argument(
'-i', '--input-file',
# Make it mandatory, difficult to over-write an existing file
required=True,
help=f'Output file'
)
parser.add_argument(
'--format',
default="msgpack",
choices=["msgpack", "json"],
help=f'Output format (default: msgpack)',
)
parser.add_argument(
'--user',
help=f'User ID to load as (default: from input)'
)
parser.add_argument(
'--collection',
help=f'Collection ID to load as (default: from input)'
)
args = parser.parse_args()
await run(**vars(args))
asyncio.run(main())

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@ -0,0 +1,190 @@
#!/usr/bin/env python3
import aiohttp
import asyncio
import msgpack
import json
import sys
import argparse
import os
async def fetch_ge(queue, user, collection, url):
async with aiohttp.ClientSession() as session:
async with session.ws_connect(f"{url}stream/graph-embeddings") as ws:
async for msg in ws:
if msg.type == aiohttp.WSMsgType.TEXT:
data = msg.json()
if user:
if data["metadata"]["user"] != user:
continue
if collection:
if data["metadata"]["collection"] != collection:
continue
await queue.put([
"ge",
{
"m": {
"i": data["metadata"]["id"],
"m": data["metadata"]["metadata"],
"u": data["metadata"]["user"],
"c": data["metadata"]["collection"],
},
"v": data["vectors"],
"e": data["entity"],
}
])
if msg.type == aiohttp.WSMsgType.ERROR:
print("Error")
break
async def fetch_triples(queue, user, collection, url):
async with aiohttp.ClientSession() as session:
async with session.ws_connect(f"{url}stream/triples") as ws:
async for msg in ws:
if msg.type == aiohttp.WSMsgType.TEXT:
data = msg.json()
if user:
if data["metadata"]["user"] != user:
continue
if collection:
if data["metadata"]["collection"] != collection:
continue
await queue.put((
"t",
{
"m": {
"i": data["metadata"]["id"],
"m": data["metadata"]["metadata"],
"u": data["metadata"]["user"],
"c": data["metadata"]["collection"],
},
"t": data["triples"],
}
))
if msg.type == aiohttp.WSMsgType.ERROR:
print("Error")
break
ge_counts = 0
t_counts = 0
async def stats():
global t_counts
global ge_counts
while True:
await asyncio.sleep(5)
print(
f"Graph embeddings: {ge_counts:10d} Triples: {t_counts:10d}"
)
async def output(queue, path, format):
global t_counts
global ge_counts
with open(path, "wb") as f:
while True:
msg = await queue.get()
if format == "msgpack":
f.write(msgpack.packb(msg, use_bin_type=True))
else:
f.write(json.dumps(msg).encode("utf-8"))
if msg[0] == "t":
t_counts += 1
else:
if msg[0] == "ge":
ge_counts += 1
async def run(**args):
q = asyncio.Queue()
ge_task = asyncio.create_task(
fetch_ge(
queue=q, user=args["user"], collection=args["collection"],
url=args["url"] + "api/v1/"
)
)
triples_task = asyncio.create_task(
fetch_triples(
queue=q, user=args["user"], collection=args["collection"],
url=args["url"] + "api/v1/"
)
)
output_task = asyncio.create_task(
output(
queue=q, path=args["output_file"], format=args["format"],
)
)
stats_task = asyncio.create_task(stats())
await output_task
await triples_task
await ge_task
await stats_task
async def main():
parser = argparse.ArgumentParser(
prog='tg-load-pdf',
description=__doc__,
)
default_url = os.getenv("TRUSTGRAPH_API", "http://localhost:8088/")
default_user = "trustgraph"
collection = "default"
parser.add_argument(
'-u', '--url',
default=default_url,
help=f'TrustGraph API URL (default: {default_url})',
)
parser.add_argument(
'-o', '--output-file',
# Make it mandatory, difficult to over-write an existing file
required=True,
help=f'Output file'
)
parser.add_argument(
'--format',
default="msgpack",
choices=["msgpack", "json"],
help=f'Output format (default: msgpack)',
)
parser.add_argument(
'--user',
help=f'User ID to filter on (default: no filter)'
)
parser.add_argument(
'--collection',
help=f'Collection ID to filter on (default: no filter)'
)
args = parser.parse_args()
await run(**vars(args))
asyncio.run(main())

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@ -39,6 +39,7 @@ setuptools.setup(
"pulsar-client",
"rdflib",
"tabulate",
"msgpack",
],
scripts=[
"scripts/tg-graph-show",
@ -54,5 +55,8 @@ setuptools.setup(
"scripts/tg-invoke-agent",
"scripts/tg-invoke-prompt",
"scripts/tg-invoke-llm",
"scripts/tg-save-kg-core",
"scripts/tg-load-kg-core",
"scripts/tg-dump-msgpack",
]
)

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@ -14,7 +14,7 @@ module = ".".join(__name__.split(".")[1:-1])
import asyncio
import argparse
from aiohttp import web
from aiohttp import web, WSMsgType
import json
import logging
import uuid
@ -47,9 +47,13 @@ from ... schema import GraphRagQuery, GraphRagResponse
from ... schema import graph_rag_request_queue
from ... schema import graph_rag_response_queue
from ... schema import TriplesQueryRequest, TriplesQueryResponse
from ... schema import TriplesQueryRequest, TriplesQueryResponse, Triples
from ... schema import triples_request_queue
from ... schema import triples_response_queue
from ... schema import triples_store_queue
from ... schema import GraphEmbeddings
from ... schema import graph_embeddings_store_queue
from ... schema import AgentRequest, AgentResponse
from ... schema import agent_request_queue
@ -84,6 +88,11 @@ def to_subgraph(x):
for t in x
]
class Running:
def __init__(self): self.running = True
def get(self): return self.running
def stop(self): self.running = False
class Publisher:
def __init__(self, pulsar_host, topic, schema=None, max_size=10,
@ -132,6 +141,7 @@ class Subscriber:
self.consumer_name = consumer_name
self.schema = schema
self.q = {}
self.full = {}
async def run(self):
while True:
@ -145,10 +155,19 @@ class Subscriber:
) as consumer:
while True:
msg = await consumer.receive()
id = msg.properties()["id"]
try:
id = msg.properties()["id"]
except:
id = None
value = msg.value()
if id in self.q:
await self.q[id].put(value)
for q in self.full.values():
await q.put(value)
except Exception as e:
print("Exception:", e, flush=True)
@ -164,6 +183,59 @@ class Subscriber:
if id in self.q:
del self.q[id]
async def subscribe_all(self, id):
q = asyncio.Queue()
self.full[id] = q
return q
async def unsubscribe_all(self, id):
if id in self.full:
del self.full[id]
def serialize_triples(message):
return {
"metadata": {
"id": message.metadata.id,
"metadata": [
{
"s": t.s.value,
"p": t.p.value,
"o": t.o.value,
}
for t in message.metadata.metadata
],
"user": message.metadata.user,
"collection": message.metadata.collection,
},
"triples": [
{
"s": t.s.value,
"p": t.p.value,
"o": t.o.value,
}
for t in message.triples
]
}
def serialize_graph_embeddings(message):
return {
"metadata": {
"id": message.metadata.id,
"metadata": [
{
"s": t.s.value,
"p": t.p.value,
"o": t.o.value,
}
for t in message.metadata.metadata
],
"user": message.metadata.user,
"collection": message.metadata.collection,
},
"vectors": message.vectors,
"entity": message.entity.value,
}
class Api:
def __init__(self, **config):
@ -243,6 +315,28 @@ class Api:
JsonSchema(EmbeddingsResponse)
)
self.triples_tap = Subscriber(
self.pulsar_host, triples_store_queue,
"api-gateway", "api-gateway",
schema=JsonSchema(Triples)
)
self.triples_pub = Publisher(
self.pulsar_host, triples_store_queue,
schema=JsonSchema(Triples)
)
self.graph_embeddings_tap = Subscriber(
self.pulsar_host, graph_embeddings_store_queue,
"api-gateway", "api-gateway",
schema=JsonSchema(GraphEmbeddings)
)
self.graph_embeddings_pub = Publisher(
self.pulsar_host, graph_embeddings_store_queue,
schema=JsonSchema(GraphEmbeddings)
)
self.document_out = Publisher(
self.pulsar_host, document_ingest_queue,
schema=JsonSchema(Document),
@ -264,6 +358,20 @@ class Api:
web.post("/api/v1/embeddings", self.embeddings),
web.post("/api/v1/load/document", self.load_document),
web.post("/api/v1/load/text", self.load_text),
web.get("/api/v1/ws", self.socket),
web.get("/api/v1/stream/triples", self.stream_triples),
web.get(
"/api/v1/stream/graph-embeddings",
self.stream_graph_embeddings
),
web.get("/api/v1/load/triples", self.load_triples),
web.get(
"/api/v1/load/graph-embeddings",
self.load_graph_embeddings
),
])
async def llm(self, request):
@ -660,6 +768,169 @@ class Api:
{ "error": str(e) }
)
async def socket(self, request):
ws = web.WebSocketResponse()
await ws.prepare(request)
async for msg in ws:
if msg.type == WSMsgType.TEXT:
if msg.data == 'close':
await ws.close()
else:
await ws.send_str(msg.data + '/answer')
elif msg.type == WSMsgType.ERROR:
print('ws connection closed with exception %s' %
ws.exception())
print('websocket connection closed')
return ws
async def stream(self, q, ws, running, fn):
while running.get():
try:
resp = await asyncio.wait_for(q.get(), 0.5)
await ws.send_json(fn(resp))
except TimeoutError:
continue
except Exception as e:
print(f"Exception: {str(e)}", flush=True)
async def stream_triples(self, request):
id = str(uuid.uuid4())
q = await self.triples_tap.subscribe_all(id)
running = Running()
ws = web.WebSocketResponse()
await ws.prepare(request)
tsk = asyncio.create_task(self.stream(
q,
ws,
running,
serialize_triples,
))
async for msg in ws:
if msg.type == WSMsgType.ERROR:
break
else:
# Ignore incoming messages
pass
running.stop()
await self.triples_tap.unsubscribe_all(id)
await tsk
return ws
async def stream_graph_embeddings(self, request):
id = str(uuid.uuid4())
q = await self.graph_embeddings_tap.subscribe_all(id)
running = Running()
ws = web.WebSocketResponse()
await ws.prepare(request)
tsk = asyncio.create_task(self.stream(
q,
ws,
running,
serialize_graph_embeddings,
))
async for msg in ws:
if msg.type == WSMsgType.ERROR:
break
else:
# Ignore incoming messages
pass
running.stop()
await self.graph_embeddings_tap.unsubscribe_all(id)
await tsk
return ws
async def load_triples(self, request):
ws = web.WebSocketResponse()
await ws.prepare(request)
async for msg in ws:
try:
if msg.type == WSMsgType.TEXT:
data = msg.json()
elt = Triples(
metadata=Metadata(
id=data["metadata"]["id"],
metadata=to_subgraph(data["metadata"]["metadata"]),
user=data["metadata"]["user"],
collection=data["metadata"]["collection"],
),
triples=to_subgraph(data["triples"]),
)
await self.triples_pub.send(None, elt)
elif msg.type == WSMsgType.ERROR:
break
except Exception as e:
print("Exception:", e)
return ws
async def load_graph_embeddings(self, request):
ws = web.WebSocketResponse()
await ws.prepare(request)
async for msg in ws:
try:
if msg.type == WSMsgType.TEXT:
data = msg.json()
elt = GraphEmbeddings(
metadata=Metadata(
id=data["metadata"]["id"],
metadata=to_subgraph(data["metadata"]["metadata"]),
user=data["metadata"]["user"],
collection=data["metadata"]["collection"],
),
entity=to_value(data["entity"]),
vectors=data["vectors"],
)
await self.graph_embeddings_pub.send(None, elt)
elif msg.type == WSMsgType.ERROR:
break
except Exception as e:
print("Exception:", e)
return ws
async def app_factory(self):
self.llm_pub_task = asyncio.create_task(self.llm_in.run())
@ -688,6 +959,22 @@ class Api:
self.embeddings_out.run()
)
self.triples_tap_task = asyncio.create_task(
self.triples_tap.run()
)
self.triples_pub_task = asyncio.create_task(
self.triples_pub.run()
)
self.graph_embeddings_tap_task = asyncio.create_task(
self.graph_embeddings_tap.run()
)
self.graph_embeddings_pub_task = asyncio.create_task(
self.graph_embeddings_pub.run()
)
self.doc_ingest_pub_task = asyncio.create_task(self.document_out.run())
self.text_ingest_pub_task = asyncio.create_task(self.text_out.run())
@ -699,7 +986,6 @@ class Api:
def run():
parser = argparse.ArgumentParser(
prog="api-gateway",
description=__doc__