建议使用批次导入数据大大缩短时间

[xiaohaoo]

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()

[agecspnt]

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