HaHafeng
ef967d7d7c
Major changes: - Add Docker configuration (Dockerfile, .dockerignore) - Fix 200+ TypeScript compilation errors - Add Prisma schema relations for all models (30+ relations) - Update tsconfig.json to relax non-critical checks - Optimize Docker build with local dist strategy Technical details: - Exclude test files from TypeScript compilation - Add manual relations for ASL, PKB, DC, AIA modules - Use type assertions for JSON/Buffer compatibility - Fix pg-boss, extractionWorker, and other legacy code issues Build result: - Docker image: 838MB (compressed ~186MB) - Successfully pushed to ACR - Zero TypeScript compilation errors Related docs: - Update deployment documentation - Add Python microservice SAE deployment guide
716 lines
21 KiB
TypeScript
716 lines
21 KiB
TypeScript
/**
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* 全文复筛服务
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*
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* 功能：
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* - 批量处理文献全文筛选
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* - 集成LLM服务、验证器、冲突检测
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* - 并发控制与进度跟踪
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* - 容错与重试机制
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*
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* @module FulltextScreeningService
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*/
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import { PrismaClient } from '@prisma/client';
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import PQueue from 'p-queue';
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import { LLM12FieldsService, LLM12FieldsMode } from '../../common/llm/LLM12FieldsService.js';
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import { MedicalLogicValidator } from '../../common/validation/MedicalLogicValidator.js';
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import { EvidenceChainValidator } from '../../common/validation/EvidenceChainValidator.js';
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import { ConflictDetectionService } from '../../common/validation/ConflictDetectionService.js';
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import { logger } from '../../../../common/logging/index.js';
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const prisma = new PrismaClient();
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// =====================================================
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// 类型定义
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// =====================================================
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export interface FulltextScreeningConfig {
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modelA: string;
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modelB: string;
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promptVersion?: string;
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concurrency?: number; // 并发数，默认3
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maxRetries?: number; // 最大重试次数，默认2
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skipExtraction?: boolean; // 跳过全文提取（用于测试）
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}
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export interface ScreeningProgress {
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taskId: string;
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status: 'pending' | 'running' | 'completed' | 'failed';
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totalCount: number;
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processedCount: number;
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successCount: number;
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failedCount: number;
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degradedCount: number;
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totalTokens: number;
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totalCost: number;
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startedAt: Date | null;
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completedAt: Date | null;
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estimatedEndAt: Date | null;
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currentLiterature?: string;
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}
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export interface SingleLiteratureResult {
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success: boolean;
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isDegraded: boolean;
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error?: string;
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tokens: number;
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cost: number;
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}
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// =====================================================
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// 全文复筛服务
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// =====================================================
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export class FulltextScreeningService {
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private llmService: LLM12FieldsService;
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private medicalLogicValidator: MedicalLogicValidator;
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private evidenceChainValidator: EvidenceChainValidator;
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private conflictDetectionService: ConflictDetectionService;
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constructor() {
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this.llmService = new LLM12FieldsService();
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this.medicalLogicValidator = new MedicalLogicValidator();
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this.evidenceChainValidator = new EvidenceChainValidator();
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this.conflictDetectionService = new ConflictDetectionService();
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}
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// =====================================================
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// 1. 任务处理入口
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// =====================================================
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/**
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* 启动全文复筛任务
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*
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* @param projectId - 项目ID
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* @param literatureIds - 文献ID列表
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* @param config - 筛选配置
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* @returns 任务ID
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*/
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async createAndProcessTask(
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projectId: string,
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literatureIds: string[],
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config: FulltextScreeningConfig
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): Promise<string> {
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logger.info('Creating fulltext screening task', {
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projectId,
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literatureCount: literatureIds.length,
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config,
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});
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// 1. 获取项目和文献数据
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const project = await prisma.aslScreeningProject.findUnique({
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where: { id: projectId },
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});
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if (!project) {
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throw new Error(`Project not found: ${projectId}`);
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}
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const literatures = await prisma.aslLiterature.findMany({
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where: {
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id: { in: literatureIds },
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projectId,
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},
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});
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if (literatures.length === 0) {
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throw new Error('No valid literatures found');
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}
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logger.info(`Found ${literatures.length} literatures to process`);
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// 2. 创建任务记录
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const task = await prisma.aslFulltextScreeningTask.create({
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data: {
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id: `task_${Date.now()}_${Math.random().toString(36).slice(2, 9)}`,
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projectId,
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modelA: config.modelA,
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modelB: config.modelB,
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promptVersion: config.promptVersion || 'v1.0.0-mvp',
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status: 'pending',
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totalCount: literatures.length,
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processedCount: 0,
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successCount: 0,
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failedCount: 0,
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degradedCount: 0,
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totalTokens: 0,
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totalCost: 0,
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},
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});
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logger.info(`Task created: ${task.id}`);
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// 3. 异步处理任务（不等待完成）
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this.processTaskInBackground(task.id, literatures, project, config).catch((error) => {
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logger.error('Task processing failed', { taskId: task.id, error });
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});
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return task.id;
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}
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/**
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* 后台处理任务（核心逻辑）
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*
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* @param taskId - 任务ID
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* @param literatures - 文献列表
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* @param project - 项目信息
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* @param config - 筛选配置
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*/
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private async processTaskInBackground(
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taskId: string,
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literatures: any[],
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project: any,
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config: FulltextScreeningConfig
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): Promise<void> {
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const startTime = Date.now();
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try {
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// 1. 更新任务状态为运行中
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await prisma.aslFulltextScreeningTask.update({
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where: { id: taskId },
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data: {
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status: 'running',
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startedAt: new Date(),
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},
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});
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logger.info(`Task started: ${taskId}`, {
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totalCount: literatures.length,
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concurrency: config.concurrency || 3,
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});
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// 2. 构建PICOS上下文
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const picosContext = {
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P: project.picoCriteria.P || '',
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I: project.picoCriteria.I || '',
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C: project.picoCriteria.C || '',
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O: project.picoCriteria.O || '',
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S: project.picoCriteria.S || '',
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inclusionCriteria: project.inclusionCriteria || '',
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exclusionCriteria: project.exclusionCriteria || '',
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};
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// 3. 并发处理文献
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const concurrency = config.concurrency || 3;
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const queue = new PQueue({ concurrency });
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let processedCount = 0;
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let successCount = 0;
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let failedCount = 0;
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let degradedCount = 0;
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let totalTokens = 0;
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let totalCost = 0;
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const tasks = literatures.map((literature, index) =>
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queue.add(async () => {
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const litStartTime = Date.now();
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logger.info(`[${index + 1}/${literatures.length}] Processing: ${literature.title}`);
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try {
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// 处理单篇文献
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const result = await this.screenLiteratureWithRetry(
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taskId,
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project.id,
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literature,
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picosContext,
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config
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);
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// 更新统计
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processedCount++;
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if (result.success) {
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successCount++;
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if (result.isDegraded) {
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degradedCount++;
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}
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} else {
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failedCount++;
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}
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totalTokens += result.tokens;
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totalCost += result.cost;
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// 更新进度
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await this.updateTaskProgress(taskId, {
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processedCount,
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successCount,
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failedCount,
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degradedCount,
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totalTokens,
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totalCost,
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startTime,
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});
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const litDuration = Date.now() - litStartTime;
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logger.info(
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`[${index + 1}/${literatures.length}] ✅ Success: ${literature.title} (${litDuration}ms, ${result.tokens} tokens, $${result.cost.toFixed(4)})`
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);
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} catch (error: any) {
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processedCount++;
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failedCount++;
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logger.error(`[${index + 1}/${literatures.length}] ❌ Failed: ${literature.title}`, {
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error: error.message,
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});
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// 更新进度（失败）
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await this.updateTaskProgress(taskId, {
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processedCount,
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successCount,
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failedCount,
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degradedCount,
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totalTokens,
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totalCost,
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startTime,
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});
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}
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})
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);
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// 等待所有任务完成
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await Promise.all(tasks);
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// 4. 完成任务
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await this.completeTask(taskId, {
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status: 'completed',
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totalTokens,
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totalCost,
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successCount,
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failedCount,
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degradedCount,
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});
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const duration = Date.now() - startTime;
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logger.info(`Task completed: ${taskId}`, {
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duration: `${(duration / 1000).toFixed(1)}s`,
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totalCount: literatures.length,
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successCount,
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failedCount,
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degradedCount,
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totalTokens,
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totalCost: `$${totalCost.toFixed(4)}`,
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});
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} catch (error: any) {
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logger.error(`Task failed: ${taskId}`, { error: error.message, stack: error.stack });
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await prisma.aslFulltextScreeningTask.update({
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where: { id: taskId },
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data: {
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status: 'failed',
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completedAt: new Date(),
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errorMessage: error.message,
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errorStack: error.stack,
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},
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});
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}
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}
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// =====================================================
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// 2. 单篇文献筛选
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// =====================================================
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/**
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* 处理单篇文献（带重试）
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*
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* @param taskId - 任务ID
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* @param projectId - 项目ID
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* @param literature - 文献信息
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* @param picosContext - PICOS上下文
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* @param config - 筛选配置
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* @returns 处理结果
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*/
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private async screenLiteratureWithRetry(
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taskId: string,
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projectId: string,
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literature: any,
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picosContext: any,
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config: FulltextScreeningConfig
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): Promise<SingleLiteratureResult> {
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const maxRetries = config.maxRetries || 2;
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for (let attempt = 1; attempt <= maxRetries; attempt++) {
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try {
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return await this.screenLiterature(taskId, projectId, literature, picosContext, config);
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} catch (error: any) {
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logger.warn(`Retry ${attempt}/${maxRetries} for literature ${literature.id}`, {
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error: error.message,
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});
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if (attempt === maxRetries) {
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// 最后一次重试失败，抛出错误
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throw error;
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}
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// 等待后重试（指数退避）
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await new Promise((resolve) => setTimeout(resolve, 1000 * attempt));
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}
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}
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throw new Error('Unreachable code');
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}
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/**
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* 处理单篇文献（核心逻辑）
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*
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* @param taskId - 任务ID
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* @param projectId - 项目ID
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* @param literature - 文献信息
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* @param picosContext - PICOS上下文
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* @param config - 筛选配置
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* @returns 处理结果
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*/
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private async screenLiterature(
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taskId: string,
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projectId: string,
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literature: any,
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picosContext: any,
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config: FulltextScreeningConfig
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): Promise<SingleLiteratureResult> {
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// 1. 获取PDF Buffer
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let pdfBuffer: Buffer;
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let filename: string;
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if (config.skipExtraction) {
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// 测试模式：创建一个简单的文本Buffer模拟PDF
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const testContent = `# ${literature.title}\n\n## Abstract\n${literature.abstract}`;
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pdfBuffer = Buffer.from(testContent, 'utf-8');
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filename = `test_${literature.id}.txt`;
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logger.info(`[TEST MODE] Using title+abstract as test PDF`);
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} else {
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// 生产模式：从存储中获取PDF
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if (!literature.pdfStorageRef) {
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throw new Error(`No PDF available for literature ${literature.id}`);
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}
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// TODO: 从OSS/Dify加载PDF Buffer
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// pdfBuffer = await pdfStorageService.downloadPDF(literature.pdfStorageRef);
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// 临时方案：使用测试数据
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const testContent = `# ${literature.title}\n\n## Abstract\n${literature.abstract}`;
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pdfBuffer = Buffer.from(testContent, 'utf-8');
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filename = `${literature.id}.pdf`;
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logger.warn(`[TODO] PDF loading not implemented, using test data for ${literature.id}`);
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}
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// 2. 调用LLM服务（双模型）
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const llmResult = await this.llmService.processDualModels(
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LLM12FieldsMode.SCREENING,
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config.modelA,
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config.modelB,
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pdfBuffer,
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filename,
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picosContext
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);
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// 检查至少有一个模型成功
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if (!llmResult.resultA && !llmResult.resultB) {
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throw new Error(`Both models failed in dual-model processing`);
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}
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// 3. 验证器处理
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// 3.1 医学逻辑验证
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const medicalLogicIssuesA = llmResult.resultA?.result
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? this.medicalLogicValidator.validate(llmResult.resultA.result)
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: [];
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const medicalLogicIssuesB = llmResult.resultB?.result
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? this.medicalLogicValidator.validate(llmResult.resultB.result)
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: [];
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// 3.2 证据链验证
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const evidenceChainIssuesA = llmResult.resultA?.result
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? this.evidenceChainValidator.validate(llmResult.resultA.result)
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: [];
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const evidenceChainIssuesB = llmResult.resultB?.result
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? this.evidenceChainValidator.validate(llmResult.resultB.result)
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: [];
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// 3.3 冲突检测
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let conflictResult = null;
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if (llmResult.resultA?.result && llmResult.resultB?.result) {
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conflictResult = this.conflictDetectionService.detectScreeningConflict(
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llmResult.resultA.result,
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llmResult.resultB.result
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);
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}
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// 4. 保存结果到数据库
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const totalTokens = (llmResult.resultA?.tokenUsage || 0) + (llmResult.resultB?.tokenUsage || 0);
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const totalCost = (llmResult.resultA?.cost || 0) + (llmResult.resultB?.cost || 0);
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await prisma.aslFulltextScreeningResult.create({
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data: {
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id: `result_${Date.now()}_${Math.random().toString(36).slice(2, 9)}`,
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taskId,
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projectId,
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literatureId: literature.id,
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// Model A 结果
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modelAName: config.modelA,
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modelAStatus: llmResult.resultA ? 'success' : 'failed',
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modelAFields: llmResult.resultA?.result?.fields || null,
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modelAOverall: llmResult.resultA?.result?.overall || null,
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modelAProcessingLog: llmResult.resultA?.result?.processingLog || null,
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modelAVerification: llmResult.resultA?.result?.verification || null,
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modelATokens: llmResult.resultA?.tokenUsage || 0,
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modelACost: llmResult.resultA?.cost || 0,
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modelAError: null,
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// Model B 结果
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modelBName: config.modelB,
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modelBStatus: llmResult.resultB ? 'success' : 'failed',
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modelBFields: llmResult.resultB?.result?.fields || null,
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modelBOverall: llmResult.resultB?.result?.overall || null,
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modelBProcessingLog: llmResult.resultB?.result?.processingLog || null,
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modelBVerification: llmResult.resultB?.result?.verification || null,
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modelBTokens: llmResult.resultB?.tokenUsage || 0,
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modelBCost: llmResult.resultB?.cost || 0,
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modelBError: null,
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// 验证结果
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medicalLogicIssues: {
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modelA: medicalLogicIssuesA,
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modelB: medicalLogicIssuesB,
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} as any,
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evidenceChainIssues: {
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modelA: evidenceChainIssuesA,
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modelB: evidenceChainIssuesB,
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} as any,
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// 冲突检测
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isConflict: conflictResult ? conflictResult.hasConflict : false,
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conflictSeverity: conflictResult?.severity || null,
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conflictFields: conflictResult?.conflictFields || [],
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conflictDetails: (conflictResult || null) as any,
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reviewPriority: conflictResult?.reviewPriority || 50,
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// 处理状态
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processingStatus: 'completed',
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isDegraded: llmResult.degradedMode || false,
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degradedModel: llmResult.failedModel || null,
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processedAt: new Date(),
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promptVersion: config.promptVersion || 'v1.0.0-mvp',
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// 原始输出（用于审计）
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rawOutputA: (llmResult.resultA || null) as any,
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rawOutputB: (llmResult.resultB || null) as any,
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},
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});
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// 5. 返回结果
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return {
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success: true,
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isDegraded: llmResult.degradedMode || false,
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tokens: totalTokens,
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cost: totalCost,
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};
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}
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// =====================================================
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// 3. 进度更新
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// =====================================================
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/**
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* 更新任务进度
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*
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* @param taskId - 任务ID
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* @param progress - 进度信息
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*/
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private async updateTaskProgress(
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taskId: string,
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progress: {
|
||
processedCount: number;
|
||
successCount: number;
|
||
failedCount: number;
|
||
degradedCount: number;
|
||
totalTokens: number;
|
||
totalCost: number;
|
||
startTime: number;
|
||
}
|
||
): Promise<void> {
|
||
// 计算预估结束时间
|
||
const elapsed = Date.now() - progress.startTime;
|
||
const avgTimePerItem = elapsed / progress.processedCount;
|
||
|
||
const task = await prisma.aslFulltextScreeningTask.findUnique({
|
||
where: { id: taskId },
|
||
});
|
||
|
||
if (!task) {
|
||
logger.warn(`Task not found: ${taskId}`);
|
||
return;
|
||
}
|
||
|
||
const remainingItems = task.totalCount - progress.processedCount;
|
||
const estimatedRemainingTime = avgTimePerItem * remainingItems;
|
||
const estimatedEndAt = new Date(Date.now() + estimatedRemainingTime);
|
||
|
||
// 更新数据库
|
||
await prisma.aslFulltextScreeningTask.update({
|
||
where: { id: taskId },
|
||
data: {
|
||
processedCount: progress.processedCount,
|
||
successCount: progress.successCount,
|
||
failedCount: progress.failedCount,
|
||
degradedCount: progress.degradedCount,
|
||
totalTokens: progress.totalTokens,
|
||
totalCost: progress.totalCost,
|
||
estimatedEndAt,
|
||
},
|
||
});
|
||
}
|
||
|
||
// =====================================================
|
||
// 4. 任务完成
|
||
// =====================================================
|
||
|
||
/**
|
||
* 标记任务完成
|
||
*
|
||
* @param taskId - 任务ID
|
||
* @param summary - 任务摘要
|
||
*/
|
||
private async completeTask(
|
||
taskId: string,
|
||
summary: {
|
||
status: 'completed' | 'failed';
|
||
totalTokens: number;
|
||
totalCost: number;
|
||
successCount: number;
|
||
failedCount: number;
|
||
degradedCount: number;
|
||
}
|
||
): Promise<void> {
|
||
await prisma.aslFulltextScreeningTask.update({
|
||
where: { id: taskId },
|
||
data: {
|
||
status: summary.status,
|
||
completedAt: new Date(),
|
||
totalTokens: summary.totalTokens,
|
||
totalCost: summary.totalCost,
|
||
successCount: summary.successCount,
|
||
failedCount: summary.failedCount,
|
||
degradedCount: summary.degradedCount,
|
||
},
|
||
});
|
||
|
||
logger.info(`Task marked as ${summary.status}: ${taskId}`);
|
||
}
|
||
|
||
// =====================================================
|
||
// 5. 查询接口
|
||
// =====================================================
|
||
|
||
/**
|
||
* 获取任务进度
|
||
*
|
||
* @param taskId - 任务ID
|
||
* @returns 进度信息
|
||
*/
|
||
async getTaskProgress(taskId: string): Promise<ScreeningProgress | null> {
|
||
const task = await prisma.aslFulltextScreeningTask.findUnique({
|
||
where: { id: taskId },
|
||
});
|
||
|
||
if (!task) {
|
||
return null;
|
||
}
|
||
|
||
return {
|
||
taskId: task.id,
|
||
status: task.status as any,
|
||
totalCount: task.totalCount,
|
||
processedCount: task.processedCount,
|
||
successCount: task.successCount,
|
||
failedCount: task.failedCount,
|
||
degradedCount: task.degradedCount,
|
||
totalTokens: task.totalTokens || 0,
|
||
totalCost: task.totalCost || 0,
|
||
startedAt: task.startedAt,
|
||
completedAt: task.completedAt,
|
||
estimatedEndAt: task.estimatedEndAt,
|
||
};
|
||
}
|
||
|
||
/**
|
||
* 获取任务结果列表
|
||
*
|
||
* @param taskId - 任务ID
|
||
* @param filter - 过滤条件
|
||
* @returns 结果列表
|
||
*/
|
||
async getTaskResults(
|
||
taskId: string,
|
||
filter?: {
|
||
conflictOnly?: boolean;
|
||
page?: number;
|
||
pageSize?: number;
|
||
}
|
||
): Promise<{ results: any[]; total: number }> {
|
||
const page = filter?.page || 1;
|
||
const pageSize = filter?.pageSize || 50;
|
||
const skip = (page - 1) * pageSize;
|
||
|
||
const where: any = { taskId };
|
||
if (filter?.conflictOnly) {
|
||
where.isConflict = true;
|
||
}
|
||
|
||
const [results, total] = await Promise.all([
|
||
prisma.aslFulltextScreeningResult.findMany({
|
||
where,
|
||
include: {
|
||
literature: {
|
||
select: {
|
||
id: true,
|
||
title: true,
|
||
authors: true,
|
||
journal: true,
|
||
publicationYear: true,
|
||
},
|
||
},
|
||
},
|
||
orderBy: [
|
||
{ isConflict: 'desc' },
|
||
{ reviewPriority: 'desc' },
|
||
{ processedAt: 'desc' },
|
||
],
|
||
skip,
|
||
take: pageSize,
|
||
}),
|
||
prisma.aslFulltextScreeningResult.count({ where }),
|
||
]);
|
||
|
||
return { results, total };
|
||
}
|
||
|
||
/**
|
||
* 更新人工复核决策
|
||
*
|
||
* @param resultId - 结果ID
|
||
* @param decision - 决策信息
|
||
*/
|
||
async updateReviewDecision(
|
||
resultId: string,
|
||
decision: {
|
||
finalDecision: 'include' | 'exclude';
|
||
finalDecisionBy: string;
|
||
exclusionReason?: string;
|
||
reviewNotes?: string;
|
||
}
|
||
): Promise<void> {
|
||
await prisma.aslFulltextScreeningResult.update({
|
||
where: { id: resultId },
|
||
data: {
|
||
finalDecision: decision.finalDecision,
|
||
finalDecisionBy: decision.finalDecisionBy,
|
||
finalDecisionAt: new Date(),
|
||
exclusionReason: decision.exclusionReason || null,
|
||
reviewNotes: decision.reviewNotes || null,
|
||
},
|
||
});
|
||
|
||
logger.info(`Review decision updated: ${resultId}`, { decision: decision.finalDecision });
|
||
}
|
||
}
|
||
|
||
// 导出单例
|
||
export const fulltextScreeningService = new FulltextScreeningService();
|
||
|