Open xiaohaoo opened 6 months ago
import concurrent import concurrent.futures import json import multiprocessing import os from py2neo import Graph, Node, Subgraph from tqdm import tqdm class MedicalGraph: def __init__(self): pass def clear(self): self.g.run("MATCH (n) DETACH DELETE n") '''读取文件''' def read_nodes(self): # 共7类节点 drugs = [] # 药品 foods = [] # 食物 checks = [] # 检查 departments = [] # 科室 producers = [] # 药品大类 diseases = [] # 疾病 symptoms = [] # 症状 disease_infos = [] # 疾病信息 # 构建节点实体关系 rels_department = [] # 科室-科室关系 rels_noteat = [] # 疾病-忌吃食物关系 rels_doeat = [] # 疾病-宜吃食物关系 rels_recommandeat = [] # 疾病-推荐吃食物关系 rels_commonddrug = [] # 疾病-通用药品关系 rels_recommanddrug = [] # 疾病-热门药品关系 rels_check = [] # 疾病-检查关系 rels_drug_producer = [] # 厂商-药物关系 rels_symptom = [] # 疾病症状关系 rels_acompany = [] # 疾病并发关系 rels_category = [] # 疾病与科室之间的关系 for data in open(self.data_path): disease_dict = {} data_json = json.loads(data) disease = data_json['name'] disease_dict['name'] = disease 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: symptoms += data_json['symptom'] for symptom in data_json['symptom']: rels_symptom.append([disease, symptom]) if 'acompany' in data_json: for acompany in data_json['acompany']: rels_acompany.append([disease, 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: rels_category.append([disease, cure_department[0]]) if len(cure_department) == 2: big = cure_department[0] small = cure_department[1] rels_department.append([small, big]) rels_category.append([disease, small]) disease_dict['cure_department'] = cure_department 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: rels_commonddrug.append([disease, drug]) drugs += common_drug if 'recommand_drug' in data_json: recommand_drug = data_json['recommand_drug'] drugs += recommand_drug for drug in recommand_drug: rels_recommanddrug.append([disease, drug]) if 'not_eat' in data_json: not_eat = data_json['not_eat'] for _not in not_eat: rels_noteat.append([disease, _not]) foods += not_eat do_eat = data_json['do_eat'] for _do in do_eat: rels_doeat.append([disease, _do]) foods += do_eat recommand_eat = data_json['recommand_eat'] for _recommand in recommand_eat: rels_recommandeat.append([disease, _recommand]) foods += recommand_eat if 'check' in data_json: check = data_json['check'] for _check in check: rels_check.append([disease, _check]) checks += check if 'drug_detail' in data_json: drug_detail = data_json['drug_detail'] producer = [i.split('(')[0] for i in drug_detail] rels_drug_producer += [[i.split('(')[0], i.split('(')[-1].replace(')', '')] for i in drug_detail] producers += producer disease_infos.append(disease_dict) return set(drugs), set(foods), set(checks), set(departments), set(producers), set(symptoms), set(diseases), disease_infos, \ rels_check, rels_recommandeat, rels_noteat, rels_doeat, rels_department, rels_commonddrug, rels_drug_producer, rels_recommanddrug, \ rels_symptom, rels_acompany, rels_category '''建立节点''' def create_node(self, label, nodes): batch_size = 1000 batches = [list(nodes)[i:i + batch_size] for i in range(0, len(nodes), batch_size)] for batch in tqdm(batches, desc=f"Creating {label} Nodes", unit="batch"): batch_nodes = [Node(label, name=node_name) for node_name in batch] self.g.create(Subgraph(batch_nodes)) '''创建知识图谱中心疾病的节点''' def create_diseases_nodes(self, disease_infos): batch_size = 1000 batches = [disease_infos[i:i + batch_size] for i in range(0, len(disease_infos), batch_size)] for batch in tqdm(batches, desc="Importing Disease Nodes", unit="batch"): batch_nodes = [ Node("Disease", name=disease_dict['name'], desc=disease_dict['desc'], prevent=disease_dict['prevent'], cause=disease_dict['cause'], easy_get=disease_dict['easy_get'], cure_lasttime=disease_dict['cure_lasttime'], cure_department=disease_dict['cure_department'], cure_way=disease_dict['cure_way'], cured_prob=disease_dict['cured_prob']) for disease_dict in batch ] self.g.create(Subgraph(batch_nodes)) '''创建知识图谱实体节点类型schema''' def create_graphnodes(self): Drugs, Foods, Checks, Departments, Producers, Symptoms, Diseases, disease_infos, rels_check, rels_recommandeat, rels_noteat, rels_doeat, rels_department, rels_commonddrug, rels_drug_producer, rels_recommanddrug, rels_symptom, rels_acompany, rels_category = self.read_nodes() self.create_diseases_nodes(disease_infos) self.create_node('Drug', Drugs) self.create_node('Food', Foods) self.create_node('Check', Checks) self.create_node('Department', Departments) self.create_node('Producer', Producers) self.create_node('Symptom', Symptoms) '''创建实体关系边''' def create_graphrels(self): Drugs, Foods, Checks, Departments, Producers, Symptoms, Diseases, disease_infos, rels_check, rels_recommandeat, rels_noteat, rels_doeat, rels_department, rels_commonddrug, rels_drug_producer, rels_recommanddrug, rels_symptom, rels_acompany, rels_category = self.read_nodes() self.create_relationship('Disease', 'Food', rels_recommandeat, 'recommand_eat', '推荐食谱') self.create_relationship('Disease', 'Food', rels_noteat, 'no_eat', '忌吃') self.create_relationship('Disease', 'Food', rels_doeat, 'do_eat', '宜吃') self.create_relationship('Department', 'Department', rels_department, 'belongs_to', '属于') self.create_relationship('Disease', 'Drug', rels_commonddrug, 'common_drug', '常用药品') self.create_relationship('Producer', 'Drug', rels_drug_producer, 'drugs_of', '生产药品') self.create_relationship('Disease', 'Drug', rels_recommanddrug, 'recommand_drug', '好评药品') self.create_relationship('Disease', 'Check', rels_check, 'need_check', '诊断检查') self.create_relationship('Disease', 'Symptom', rels_symptom, 'has_symptom', '症状') self.create_relationship('Disease', 'Disease', rels_acompany, 'acompany_with', '并发症') self.create_relationship('Disease', 'Department', rels_category, 'belongs_to', '所属科室') '''创建实体关联边''' def create_relationship(self, start_node, end_node, edges, rel_type, rel_name): batch_size = 10000 set_edges = set(['###'.join(edge) for edge in edges]) batches = [list(set_edges)[i:i + batch_size] for i in range(0, len(set_edges), batch_size)] executor = concurrent.futures.ThreadPoolExecutor(max_workers=min(multiprocessing.cpu_count(), 4)) tasks = [ lambda: ( tx := self.g.begin(), [ tx.run( f"MATCH (p:{start_node}), (q:{end_node}) " f"WHERE p.name='{p}' AND q.name='{q}' " f"CREATE (p)-[rel:{rel_type} {{name:'{rel_name}'}}]->(q)" ) for edge in batch for p, q in [edge.split('###')] ], self.g.commit(tx) ) for batch in tqdm(batches, desc=f"Creating {rel_type} Relationships", unit="batch") ] executor.map(lambda task: task(), tasks) executor.shutdown() '''导出数据''' def export_data(self): Drugs, Foods, Checks, Departments, Producers, Symptoms, Diseases, disease_infos, rels_check, rels_recommandeat, rels_noteat, rels_doeat, rels_department, rels_commonddrug, rels_drug_producer, rels_recommanddrug, rels_symptom, rels_acompany, rels_category = self.read_nodes() f_drug = open('drug.txt', 'w+') f_food = open('food.txt', 'w+') f_check = open('check.txt', 'w+') f_department = open('department.txt', 'w+') f_producer = open('producer.txt', 'w+') f_symptom = open('symptoms.txt', 'w+') f_disease = open('disease.txt', 'w+') f_drug.write('\n'.join(list(Drugs))) f_food.write('\n'.join(list(Foods))) f_check.write('\n'.join(list(Checks))) f_department.write('\n'.join(list(Departments))) f_producer.write('\n'.join(list(Producers))) f_symptom.write('\n'.join(list(Symptoms))) f_disease.write('\n'.join(list(Diseases))) f_drug.close() f_food.close() f_check.close() f_department.close() f_producer.close() f_symptom.close() f_disease.close() if __name__ == '__main__': handler = MedicalGraph() handler.clear() print("step1:导入图谱节点中") handler.create_graphnodes() print("step2:导入图谱边中") handler.create_graphrels()
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