mirror of
https://github.com/trustgraph-ai/trustgraph.git
synced 2026-05-26 07:45:13 +02:00
Feature/memgraph optim (#193)
* Separate memgraph query/write modules to optimise for memgraph * Used 1GB memory for Memgraph * Deployed specialised memgraph query/write processors, created memgraph indexes * One triple is loaded as a single transaction * Fixed index creation
This commit is contained in:
cybermaggedon
GitHub
parent
e3d06ab80b
commit
bffaf62490
12 changed files with 651 additions and 4 deletions
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from . service import *
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7
trustgraph-flow/trustgraph/query/triples/memgraph/__main__.py
Executable file
7
trustgraph-flow/trustgraph/query/triples/memgraph/__main__.py
Executable file
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#!/usr/bin/env python3
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from . hf import run
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if __name__ == '__main__':
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run()
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357
trustgraph-flow/trustgraph/query/triples/memgraph/service.py
Executable file
357
trustgraph-flow/trustgraph/query/triples/memgraph/service.py
Executable file
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"""
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Triples query service for memgraph.
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Input is a (s, p, o) triple, some values may be null. Output is a list of
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triples.
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"""
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from neo4j import GraphDatabase
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from .... schema import TriplesQueryRequest, TriplesQueryResponse, Error
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from .... schema import Value, Triple
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from .... schema import triples_request_queue
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from .... schema import triples_response_queue
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from .... base import ConsumerProducer
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module = ".".join(__name__.split(".")[1:-1])
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default_input_queue = triples_request_queue
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default_output_queue = triples_response_queue
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default_subscriber = module
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default_graph_host = 'bolt://memgraph:7687'
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default_username = 'memgraph'
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default_password = 'password'
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default_database = 'memgraph'
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class Processor(ConsumerProducer):
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def __init__(self, **params):
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input_queue = params.get("input_queue", default_input_queue)
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output_queue = params.get("output_queue", default_output_queue)
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subscriber = params.get("subscriber", default_subscriber)
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graph_host = params.get("graph_host", default_graph_host)
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username = params.get("username", default_username)
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password = params.get("password", default_password)
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database = params.get("database", default_database)
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super(Processor, self).__init__(
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**params | {
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"input_queue": input_queue,
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"output_queue": output_queue,
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"subscriber": subscriber,
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"input_schema": TriplesQueryRequest,
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"output_schema": TriplesQueryResponse,
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"graph_host": graph_host,
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}
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)
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self.db = database
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self.io = GraphDatabase.driver(graph_host, auth=(username, password))
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def create_value(self, ent):
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if ent.startswith("http://") or ent.startswith("https://"):
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return Value(value=ent, is_uri=True)
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else:
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return Value(value=ent, is_uri=False)
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def handle(self, msg):
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try:
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v = msg.value()
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# Sender-produced ID
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id = msg.properties()["id"]
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print(f"Handling input {id}...", flush=True)
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triples = []
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if v.s is not None:
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if v.p is not None:
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if v.o is not None:
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# SPO
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node {uri: $src})-[rel:Rel {uri: $rel}]->(dest:Literal {value: $value}) "
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"RETURN $src as src",
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src=v.s.value, rel=v.p.value, value=v.o.value,
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database_=self.db,
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)
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for rec in records:
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triples.append((v.s.value, v.p.value, v.o.value))
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node {uri: $src})-[rel:Rel {uri: $rel}]->(dest:Node {uri: $uri}) "
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"RETURN $src as src",
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src=v.s.value, rel=v.p.value, uri=v.o.value,
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database_=self.db,
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)
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for rec in records:
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triples.append((v.s.value, v.p.value, v.o.value))
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else:
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# SP
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node {uri: $src})-[rel:Rel {uri: $rel}]->(dest:Literal) "
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"RETURN dest.value as dest",
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src=v.s.value, rel=v.p.value,
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database_=self.db,
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)
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for rec in records:
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data = rec.data()
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triples.append((v.s.value, v.p.value, data["dest"]))
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node {uri: $src})-[rel:Rel {uri: $rel}]->(dest:Node) "
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"RETURN dest.uri as dest",
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src=v.s.value, rel=v.p.value,
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database_=self.db,
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)
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for rec in records:
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data = rec.data()
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triples.append((v.s.value, v.p.value, data["dest"]))
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else:
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if v.o is not None:
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# SO
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node {uri: $src})-[rel:Rel]->(dest:Literal {value: $value}) "
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"RETURN rel.uri as rel",
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src=v.s.value, value=v.o.value,
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database_=self.db,
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)
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for rec in records:
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data = rec.data()
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triples.append((v.s.value, data["rel"], v.o.value))
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node {uri: $src})-[rel:Rel]->(dest:Node {uri: $uri}) "
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"RETURN rel.uri as rel",
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src=v.s.value, uri=v.o.value,
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database_=self.db,
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)
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for rec in records:
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data = rec.data()
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triples.append((v.s.value, data["rel"], v.o.value))
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else:
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# S
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node {uri: $src})-[rel:Rel]->(dest:Literal) "
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"RETURN rel.uri as rel, dest.value as dest",
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src=v.s.value,
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database_=self.db,
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)
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for rec in records:
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data = rec.data()
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triples.append((v.s.value, data["rel"], data["dest"]))
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node {uri: $src})-[rel:Rel]->(dest:Node) "
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"RETURN rel.uri as rel, dest.uri as dest",
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src=v.s.value,
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database_=self.db,
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)
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for rec in records:
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data = rec.data()
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triples.append((v.s.value, data["rel"], data["dest"]))
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else:
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if v.p is not None:
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if v.o is not None:
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# PO
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node)-[rel:Rel {uri: $uri}]->(dest:Literal {value: $value}) "
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"RETURN src.uri as src",
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uri=v.p.value, value=v.o.value,
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database_=self.db,
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)
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for rec in records:
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data = rec.data()
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triples.append((data["src"], v.p.value, v.o.value))
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node)-[rel:Rel {uri: $uri}]->(dest:Node {uri: $uri}) "
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"RETURN src.uri as src",
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uri=v.p.value, dest=v.o.value,
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database_=self.db,
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)
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for rec in records:
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data = rec.data()
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triples.append((data["src"], v.p.value, v.o.value))
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else:
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# P
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node)-[rel:Rel {uri: $uri}]->(dest:Literal) "
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"RETURN src.uri as src, dest.value as dest",
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uri=v.p.value,
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database_=self.db,
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)
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for rec in records:
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data = rec.data()
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triples.append((data["src"], v.p.value, data["dest"]))
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node)-[rel:Rel {uri: $uri}]->(dest:Node) "
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"RETURN src.uri as src, dest.uri as dest",
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uri=v.p.value,
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database_=self.db,
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)
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for rec in records:
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data = rec.data()
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triples.append((data["src"], v.p.value, data["dest"]))
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else:
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if v.o is not None:
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# O
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node)-[rel:Rel]->(dest:Literal {value: $value}) "
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"RETURN src.uri as src, rel.uri as rel",
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value=v.o.value,
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database_=self.db,
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)
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for rec in records:
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data = rec.data()
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triples.append((data["src"], data["rel"], v.o.value))
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node)-[rel:Rel]->(dest:Node {uri: $uri}) "
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"RETURN src.uri as src, rel.uri as rel",
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uri=v.o.value,
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database_=self.db,
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)
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for rec in records:
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data = rec.data()
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triples.append((data["src"], data["rel"], v.o.value))
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else:
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# *
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node)-[rel:Rel]->(dest:Literal) "
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"RETURN src.uri as src, rel.uri as rel, dest.value as dest",
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database_=self.db,
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)
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for rec in records:
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data = rec.data()
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triples.append((data["src"], data["rel"], data["dest"]))
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records, summary, keys = self.io.execute_query(
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"MATCH (src:Node)-[rel:Rel]->(dest:Node) "
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"RETURN src.uri as src, rel.uri as rel, dest.uri as dest",
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database_=self.db,
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)
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for rec in records:
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data = rec.data()
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triples.append((data["src"], data["rel"], data["dest"]))
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triples = [
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Triple(
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s=self.create_value(t[0]),
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p=self.create_value(t[1]),
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o=self.create_value(t[2])
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)
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for t in triples
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]
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print("Send response...", flush=True)
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r = TriplesQueryResponse(triples=triples, error=None)
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self.producer.send(r, properties={"id": id})
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print("Done.", flush=True)
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except Exception as e:
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print(f"Exception: {e}")
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print("Send error response...", flush=True)
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r = TriplesQueryResponse(
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error=Error(
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type = "llm-error",
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message = str(e),
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),
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response=None,
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)
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self.producer.send(r, properties={"id": id})
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self.consumer.acknowledge(msg)
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@staticmethod
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def add_args(parser):
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ConsumerProducer.add_args(
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parser, default_input_queue, default_subscriber,
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default_output_queue,
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)
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parser.add_argument(
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'-g', '--graph-host',
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default=default_graph_host,
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help=f'Graph host (default: {default_graph_host})'
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)
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parser.add_argument(
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'--username',
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default=default_username,
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help=f'Memgraph username (default: {default_username})'
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)
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parser.add_argument(
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'--password',
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default=default_password,
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help=f'Memgraph password (default: {default_password})'
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)
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parser.add_argument(
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'--database',
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default=default_database,
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help=f'Memgraph database (default: {default_database})'
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)
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def run():
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Processor.start(module, __doc__)
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"""
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Triples query service. Input is a (s, p, o) triple, some values may be
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null. Output is a list of triples.
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Triples query service for neo4j.
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Input is a (s, p, o) triple, some values may be null. Output is a list of
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triples.
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"""
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from neo4j import GraphDatabase
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from . write import *
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7
trustgraph-flow/trustgraph/storage/triples/memgraph/__main__.py
Executable file
7
trustgraph-flow/trustgraph/storage/triples/memgraph/__main__.py
Executable file
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#!/usr/bin/env python3
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from . write import run
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if __name__ == '__main__':
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run()
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252
trustgraph-flow/trustgraph/storage/triples/memgraph/write.py
Executable file
252
trustgraph-flow/trustgraph/storage/triples/memgraph/write.py
Executable file
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"""
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Graph writer. Input is graph edge. Writes edges to Cassandra graph.
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"""
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import pulsar
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import base64
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import os
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import argparse
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import time
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from neo4j import GraphDatabase
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from .... schema import Triples
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from .... schema import triples_store_queue
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from .... log_level import LogLevel
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from .... base import Consumer
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module = ".".join(__name__.split(".")[1:-1])
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default_input_queue = triples_store_queue
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default_subscriber = module
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default_graph_host = 'bolt://memgraph:7687'
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default_username = 'memgraph'
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default_password = 'password'
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default_database = 'memgraph'
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class Processor(Consumer):
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def __init__(self, **params):
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input_queue = params.get("input_queue", default_input_queue)
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subscriber = params.get("subscriber", default_subscriber)
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graph_host = params.get("graph_host", default_graph_host)
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username = params.get("username", default_username)
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password = params.get("password", default_password)
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database = params.get("database", default_database)
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super(Processor, self).__init__(
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**params | {
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"input_queue": input_queue,
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"subscriber": subscriber,
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"input_schema": Triples,
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"graph_host": graph_host,
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}
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)
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self.db = database
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self.io = GraphDatabase.driver(graph_host, auth=(username, password))
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with self.io.session(database=self.db) as session:
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self.create_indexes(session)
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def create_indexes(self, session):
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print("Create indexes...", flush=True)
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try:
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session.run(
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"CREATE INDEX ON :Node",
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)
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except Exception as e:
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print(e, flush=True)
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# Maybe index already exists
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print("Index create failure ignored", flush=True)
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try:
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session.run(
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"CREATE INDEX ON :Node(uri)"
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)
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except Exception as e:
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print(e, flush=True)
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# Maybe index already exists
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print("Index create failure ignored", flush=True)
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try:
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session.run(
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"CREATE INDEX ON :Literal",
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)
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except Exception as e:
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print(e, flush=True)
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# Maybe index already exists
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print("Index create failure ignored", flush=True)
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try:
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session.run(
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"CREATE INDEX ON :Literal(value)"
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)
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except Exception as e:
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print(e, flush=True)
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# Maybe index already exists
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print("Index create failure ignored", flush=True)
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print("Index creation done", flush=True)
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def create_node(self, uri):
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print("Create node", uri)
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summary = self.io.execute_query(
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"MERGE (n:Node {uri: $uri})",
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uri=uri,
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database_=self.db,
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).summary
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print("Created {nodes_created} nodes in {time} ms.".format(
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nodes_created=summary.counters.nodes_created,
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time=summary.result_available_after
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))
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||||
|
||||
def create_literal(self, value):
|
||||
|
||||
print("Create literal", value)
|
||||
|
||||
summary = self.io.execute_query(
|
||||
"MERGE (n:Literal {value: $value})",
|
||||
value=value,
|
||||
database_=self.db,
|
||||
).summary
|
||||
|
||||
print("Created {nodes_created} nodes in {time} ms.".format(
|
||||
nodes_created=summary.counters.nodes_created,
|
||||
time=summary.result_available_after
|
||||
))
|
||||
|
||||
def relate_node(self, src, uri, dest):
|
||||
|
||||
print("Create node rel", src, uri, dest)
|
||||
|
||||
summary = self.io.execute_query(
|
||||
"MATCH (src:Node {uri: $src}) "
|
||||
"MATCH (dest:Node {uri: $dest}) "
|
||||
"MERGE (src)-[:Rel {uri: $uri}]->(dest)",
|
||||
src=src, dest=dest, uri=uri,
|
||||
database_=self.db,
|
||||
).summary
|
||||
|
||||
print("Created {nodes_created} nodes in {time} ms.".format(
|
||||
nodes_created=summary.counters.nodes_created,
|
||||
time=summary.result_available_after
|
||||
))
|
||||
|
||||
def relate_literal(self, src, uri, dest):
|
||||
|
||||
print("Create literal rel", src, uri, dest)
|
||||
|
||||
summary = self.io.execute_query(
|
||||
"MATCH (src:Node {uri: $src}) "
|
||||
"MATCH (dest:Literal {value: $dest}) "
|
||||
"MERGE (src)-[:Rel {uri: $uri}]->(dest)",
|
||||
src=src, dest=dest, uri=uri,
|
||||
database_=self.db,
|
||||
).summary
|
||||
|
||||
print("Created {nodes_created} nodes in {time} ms.".format(
|
||||
nodes_created=summary.counters.nodes_created,
|
||||
time=summary.result_available_after
|
||||
))
|
||||
|
||||
def create_triple(self, tx, t):
|
||||
|
||||
# Create new s node with given uri, if not exists
|
||||
result = tx.run(
|
||||
"MERGE (n:Node {uri: $uri})",
|
||||
uri=t.s.value
|
||||
)
|
||||
|
||||
if t.o.is_uri:
|
||||
|
||||
# Create new o node with given uri, if not exists
|
||||
result = tx.run(
|
||||
"MERGE (n:Node {uri: $uri})",
|
||||
uri=t.o.value
|
||||
)
|
||||
|
||||
result = tx.run(
|
||||
"MATCH (src:Node {uri: $src}) "
|
||||
"MATCH (dest:Node {uri: $dest}) "
|
||||
"MERGE (src)-[:Rel {uri: $uri}]->(dest)",
|
||||
src=t.s.value, dest=t.o.value, uri=t.p.value,
|
||||
)
|
||||
|
||||
else:
|
||||
|
||||
# Create new o literal with given uri, if not exists
|
||||
result = tx.run(
|
||||
"MERGE (n:Literal {value: $value})",
|
||||
value=t.o.value
|
||||
)
|
||||
|
||||
result = tx.run(
|
||||
"MATCH (src:Node {uri: $src}) "
|
||||
"MATCH (dest:Literal {value: $dest}) "
|
||||
"MERGE (src)-[:Rel {uri: $uri}]->(dest)",
|
||||
src=t.s.value, dest=t.o.value, uri=t.p.value,
|
||||
)
|
||||
|
||||
def handle(self, msg):
|
||||
|
||||
v = msg.value()
|
||||
|
||||
for t in v.triples:
|
||||
|
||||
# self.create_node(t.s.value)
|
||||
|
||||
# if t.o.is_uri:
|
||||
# self.create_node(t.o.value)
|
||||
# self.relate_node(t.s.value, t.p.value, t.o.value)
|
||||
# else:
|
||||
# self.create_literal(t.o.value)
|
||||
# self.relate_literal(t.s.value, t.p.value, t.o.value)
|
||||
|
||||
with self.io.session(database=self.db) as session:
|
||||
session.execute_write(self.create_triple, t)
|
||||
|
||||
@staticmethod
|
||||
def add_args(parser):
|
||||
|
||||
Consumer.add_args(
|
||||
parser, default_input_queue, default_subscriber,
|
||||
)
|
||||
|
||||
parser.add_argument(
|
||||
'-g', '--graph_host',
|
||||
default=default_graph_host,
|
||||
help=f'Graph host (default: {default_graph_host})'
|
||||
)
|
||||
|
||||
parser.add_argument(
|
||||
'--username',
|
||||
default=default_username,
|
||||
help=f'Memgraph username (default: {default_username})'
|
||||
)
|
||||
|
||||
parser.add_argument(
|
||||
'--password',
|
||||
default=default_password,
|
||||
help=f'Memgraph password (default: {default_password})'
|
||||
)
|
||||
|
||||
parser.add_argument(
|
||||
'--database',
|
||||
default=default_database,
|
||||
help=f'Memgraph database (default: {default_database})'
|
||||
)
|
||||
|
||||
def run():
|
||||
|
||||
Processor.start(module, __doc__)
|
||||
|
||||
Loading…
Add table
Add a link
Reference in a new issue