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#encoding:utf8
import os
import re
import json
import codecs
import threading
from py2neo import Graph
import pandas as pd
import numpy as np
from tqdm import tqdm
### Get data Info
def print_data_info(data_path):
triples = []
i = 0
with open(data_path,'r',encoding='utf8') as f:
for line in f.readlines():
data = json.loads(line)
print(json.dumps(data, sort_keys=True, indent=4, separators=(', ', ': '),ensure_ascii=False))
i += 1
if i >=5:
break
return triples
### Extraction Object
class MedicalExtractor(object):
def __init__(self):
super(MedicalExtractor, self).__init__()
self.graph = Graph(
host="127.0.0.1",
http_port=7474,
user="neo4j",
password="123456")
# 共8类节点
self.drugs = [] # 药品
self.recipes = [] #菜谱
self.foods = [] # 食物
self.checks = [] # 检查
self.departments = [] #科室
self.producers = [] #药企
self.diseases = [] #疾病
self.symptoms = []#症状
self.disease_infos = []#疾病信息
# 构建节点实体关系
self.rels_department = [] # 科室－科室关系
self.rels_noteat = [] # 疾病－忌吃食物关系
self.rels_doeat = [] # 疾病－宜吃食物关系
self.rels_recommandeat = [] # 疾病－推荐吃食物关系
self.rels_commonddrug = [] # 疾病－通用药品关系
self.rels_recommanddrug = [] # 疾病－热门药品关系
self.rels_check = [] # 疾病－检查关系
self.rels_drug_producer = [] # 厂商－药物关系
self.rels_symptom = [] #疾病症状关系
self.rels_acompany = [] # 疾病并发关系
self.rels_category = [] # 疾病与科室之间的关系
def extract_triples(self,data_path):
print("从json文件中转换抽取三元组")
with open(data_path,'r',encoding='utf8') as f:
for line in tqdm(f.readlines(),ncols=80):
data_json = json.loads(line)
disease_dict = {}
disease = data_json['name']
disease_dict['name'] = disease
self.diseases.append(disease)
disease_dict['desc'] = ''
disease_dict['prevent'] = ''
disease_dict['cause'] = ''
disease_dict['easy_get'] = ''
disease_dict['cure_department'] = ''
disease_dict['cure_way'] = ''
disease_dict['cure_lasttime'] = ''
disease_dict['symptom'] = ''
disease_dict['cured_prob'] = ''
if 'symptom' in data_json:
self.symptoms += data_json['symptom']
for symptom in data_json['symptom']:
self.rels_symptom.append([disease,'has_symptom', symptom])
if 'acompany' in data_json:
for acompany in data_json['acompany']:
self.rels_acompany.append([disease,'acompany_with', acompany])
self.diseases.append(acompany)
if 'desc' in data_json:
disease_dict['desc'] = data_json['desc']
if 'prevent' in data_json:
disease_dict['prevent'] = data_json['prevent']
if 'cause' in data_json:
disease_dict['cause'] = data_json['cause']
if 'get_prob' in data_json:
disease_dict['get_prob'] = data_json['get_prob']
if 'easy_get' in data_json:
disease_dict['easy_get'] = data_json['easy_get']
if 'cure_department' in data_json:
cure_department = data_json['cure_department']
if len(cure_department) == 1:
self.rels_category.append([disease, 'cure_department',cure_department[0]])
if len(cure_department) == 2:
big = cure_department[0]
small = cure_department[1]
self.rels_department.append([small,'belongs_to', big])
self.rels_category.append([disease,'cure_department', small])
disease_dict['cure_department'] = cure_department
self.departments += cure_department
if 'cure_way' in data_json:
disease_dict['cure_way'] = data_json['cure_way']
if 'cure_lasttime' in data_json:
disease_dict['cure_lasttime'] = data_json['cure_lasttime']
if 'cured_prob' in data_json:
disease_dict['cured_prob'] = data_json['cured_prob']
if 'common_drug' in data_json:
common_drug = data_json['common_drug']
for drug in common_drug:
self.rels_commonddrug.append([disease,'has_common_drug', drug])
self.drugs += common_drug
if 'recommand_drug' in data_json:
recommand_drug = data_json['recommand_drug']
self.drugs += recommand_drug
for drug in recommand_drug:
self.rels_recommanddrug.append([disease,'recommand_drug', drug])
if 'not_eat' in data_json:
not_eat = data_json['not_eat']
for _not in not_eat:
self.rels_noteat.append([disease,'not_eat', _not])
self.foods += not_eat
do_eat = data_json['do_eat']
for _do in do_eat:
self.rels_doeat.append([disease,'do_eat', _do])
self.foods += do_eat
if 'recommand_eat' in data_json:
recommand_eat = data_json['recommand_eat']
for _recommand in recommand_eat:
self.rels_recommandeat.append([disease,'recommand_recipes', _recommand])
self.recipes += recommand_eat
if 'check' in data_json:
check = data_json['check']
for _check in check:
self.rels_check.append([disease, 'need_check', _check])
self.checks += check
if 'drug_detail' in data_json:
for det in data_json['drug_detail']:
det_spilt = det.split('(')
if len(det_spilt) == 2:
p,d = det_spilt
d = d.rstrip(')')
if p.find(d) > 0:
p = p.rstrip(d)
self.producers.append(p)
self.drugs.append(d)
self.rels_drug_producer.append([p,'production',d])
else:
d = det_spilt[0]
self.drugs.append(d)
self.disease_infos.append(disease_dict)
def write_nodes(self,entitys,entity_type):
print("写入 {0} 实体".format(entity_type))
for node in tqdm(set(entitys),ncols=80):
cql = """MERGE(n:{label}{{name:'{entity_name}'}})""".format(
label=entity_type,entity_name=node.replace("'",""))
try:
self.graph.run(cql)
except Exception as e:
print(e)
print(cql)
def write_edges(self,triples,head_type,tail_type):
print("写入 {0} 关系".format(triples[0][1]))
for head,relation,tail in tqdm(triples,ncols=80):
cql = """MATCH(p:{head_type}),(q:{tail_type})
WHERE p.name='{head}' AND q.name='{tail}'
MERGE (p)-[r:{relation}]->(q)""".format(
head_type=head_type,tail_type=tail_type,head=head.replace("'",""),
tail=tail.replace("'",""),relation=relation)
try:
self.graph.run(cql)
except Exception as e:
print(e)
print(cql)
def set_attributes(self,entity_infos,etype):
print("写入 {0} 实体的属性".format(etype))
for e_dict in tqdm(entity_infos[892:],ncols=80):
name = e_dict['name']
del e_dict['name']
for k,v in e_dict.items():
if k in ['cure_department','cure_way']:
cql = """MATCH (n:{label})
WHERE n.name='{name}'
set n.{k}={v}""".format(label=etype,name=name.replace("'",""),k=k,v=v)
else:
cql = """MATCH (n:{label})
WHERE n.name='{name}'
set n.{k}='{v}'""".format(label=etype,name=name.replace("'",""),k=k,v=v.replace("'","").replace("\n",""))
try:
self.graph.run(cql)
except Exception as e:
print(e)
print(cql)
def create_entitys(self):
self.write_nodes(self.drugs,'药品')
self.write_nodes(self.recipes,'菜谱')
self.write_nodes(self.foods,'食物')
self.write_nodes(self.checks,'检查')
self.write_nodes(self.departments,'科室')
self.write_nodes(self.producers,'药企')
self.write_nodes(self.diseases,'疾病')
self.write_nodes(self.symptoms,'症状')
def create_relations(self):
self.write_edges(self.rels_department,'科室','科室')
self.write_edges(self.rels_noteat,'疾病','食物')
self.write_edges(self.rels_doeat,'疾病','食物')
self.write_edges(self.rels_recommandeat,'疾病','菜谱')
self.write_edges(self.rels_commonddrug,'疾病','药品')
self.write_edges(self.rels_recommanddrug,'疾病','药品')
self.write_edges(self.rels_check,'疾病','检查')
self.write_edges(self.rels_drug_producer,'药企','药品')
self.write_edges(self.rels_symptom,'疾病','症状')
self.write_edges(self.rels_acompany,'疾病','疾病')
self.write_edges(self.rels_category,'疾病','科室')
def set_diseases_attributes(self):
t=threading.Thread(target=self.set_attributes,args=(self.disease_infos,"疾病"))
t.setDaemon(False)
t.start()
def export_data(self,data,path):
if isinstance(data[0],str):
data = sorted([d.strip("...") for d in set(data)])
with codecs.open(path, 'w', encoding='utf-8') as f:
json.dump(data, f, indent=4, ensure_ascii=False)
def export_entitys_relations(self):
self.export_data(self.drugs,'./graph_data/drugs.json')
self.export_data(self.recipes,'./graph_data/recipes.json')
self.export_data(self.foods,'./graph_data/foods.json')
self.export_data(self.checks,'./graph_data/checks.json')
self.export_data(self.departments,'./graph_data/departments.json')
self.export_data(self.producers,'./graph_data/producers.json')
self.export_data(self.diseases,'./graph_data/diseases.json')
self.export_data(self.symptoms,'./graph_data/symptoms.json')
self.export_data(self.rels_department,'./graph_data/rels_department.json')
self.export_data(self.rels_noteat,'./graph_data/rels_noteat.json')
self.export_data(self.rels_doeat,'./graph_data/rels_doeat.json')
self.export_data(self.rels_recommandeat,'./graph_data/rels_recommandeat.json')
self.export_data(self.rels_commonddrug,'./graph_data/rels_commonddrug.json')
self.export_data(self.rels_recommanddrug,'./graph_data/rels_recommanddrug.json')
self.export_data(self.rels_check,'./graph_data/rels_check.json')
self.export_data(self.rels_drug_producer,'./graph_data/rels_drug_producer.json')
self.export_data(self.rels_symptom,'./graph_data/rels_symptom.json')
self.export_data(self.rels_acompany,'./graph_data/rels_acompany.json')
self.export_data(self.rels_category,'./graph_data/rels_category.json')
if __name__ == '__main__':
path = "./graph_data/medical.json"
extractor = MedicalExtractor()
extractor.extract_triples(path)
extractor.export_entitys_relations()
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