Chulinz's picture
ICJ Citation Graph release with Parquet and Docker runtime
daa5e64
Raw History Blame Contribute Delete
2.17 kB
import os
import re
from neo4j import GraphDatabase
def identifier(value):
if not re.fullmatch(r'[A-Za-z_][A-Za-z0-9_]*', value):
raise ValueError('Invalid Cypher identifier: ' + value)
return '`' + value + '`'
class Graph:
def __init__(self):
self.driver = GraphDatabase.driver(os.getenv('NEO4J_URI', 'bolt://neo4j:7687'), auth=(os.getenv('NEO4J_USERNAME', 'neo4j'), os.environ['NEO4J_PASSWORD']), notifications_min_severity='OFF')
self.database = os.getenv('NEO4J_DATABASE', 'neo4j')
def run(self, query, **params):
with self.driver.session(database=self.database) as session:
return [dict(record) for record in session.run(query, **params)]
def check_source(self, target, prop, source):
p = identifier(prop)
marker = identifier(prop + '__source')
mismatch = self.run(f'MATCH (n:{target.label}) WHERE n.{p} IS NOT NULL AND (n.{marker} IS NULL OR n.{marker} <> $source) RETURN count(n) AS n', source=source)[0]['n']
if mismatch:
raise ValueError(f'{mismatch} existing vectors have different or unknown provenance. Use a different --property or a fresh graph.')
def missing(self, target, ids, prop):
rows = self.run(f'UNWIND $ids AS key OPTIONAL MATCH (n:{target.label} {{{target.key}:key}}) RETURN key,n IS NOT NULL AS found,n.{identifier(prop)} IS NULL AS missing', ids=ids)
if len(rows) != len(ids) or not all(row['found'] for row in rows):
raise ValueError('Parquet keys do not match this graph snapshot.')
return {row['key'] for row in rows if row['missing']}
def write(self, target, prop, source, rows):
if not rows:
return
result = self.run(f'UNWIND $rows AS row MATCH (n:{target.label} {{{target.key}:row.key}}) WHERE n.{identifier(prop)} IS NULL SET n.{identifier(prop)}=row.vector,n.{identifier(prop + "__source")}=$source RETURN count(n) AS n', rows=rows, source=source)
if result[0]['n'] != len(rows):
raise RuntimeError('Graph changed during writing; stop concurrent vector writers and retry.')
def close(self):
self.driver.close()