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16 Commits

Author SHA1 Message Date
HaHafeng
bf10dec4c8 docs(ssa): Complete intelligent dialogue and tool system architecture design 
Architecture Design:
- Add intent recognition and dialogue architecture design (Intent Router + DataContext)
- Add tool system planning (4-layer 7-tool fusion solution: READ/INTERACT/THINK/ACT)
- Add 4-layer 7-tool implementation mechanism details (Conversation Layer LLM + Node.js orchestration)

Development Plan (v1.2):
- Create 6-phase development plan (134h/22 days) for intelligent dialogue system
- Add 8 architectural constraints (C1-C8): no Function Calling, Postgres-Only cache,
  streaming output, context guard, Zod dynamic validation
- Correct Session Blackboard to use CacheFactory (Postgres-Only, no Redis)

Status Updates:
- Update SSA module status: QPER complete + dialogue architecture design complete
- Update system-level status: add SSA architecture design milestone

Other:
- R tools minor fixes (chi_square, correlation, logistic_binary, mann_whitney, t_test_paired)
- Frontend AIA chat workspace style adjustment

Co-authored-by: Cursor <cursoragent@cursor.com>
 2026-02-22 10:05:14 +08:00
HaHafeng
371e1c069c feat(ssa): Complete QPER architecture - Query, Planner, Execute, Reflection layers 
Implement the full QPER intelligent analysis pipeline:

- Phase E+: Block-based standardization for all 7 R tools, DynamicReport renderer, Word export enhancement

- Phase Q: LLM intent parsing with dynamic Zod validation against real column names, ClarificationCard component, DataProfile is_id_like tagging

- Phase P: ConfigLoader with Zod schema validation and hot-reload API, DecisionTableService (4-dimension matching), FlowTemplateService with EPV protection, PlannedTrace audit output

- Phase R: ReflectionService with statistical slot injection, sensitivity analysis conflict rules, ConclusionReport with section reveal animation, conclusion caching API, graceful R error classification

End-to-end test: 40/40 passed across two complete analysis scenarios.

Co-authored-by: Cursor <cursoragent@cursor.com>
 2026-02-21 18:15:53 +08:00
HaHafeng
49b5c37cb1 feat(ssa): Complete T-test end-to-end testing with 9 bug fixes - Phase 1 core 85% complete. R service: missing value auto-filter. Backend: error handling, variable matching, dynamic filename. Frontend: module activation, session isolation, error propagation. Full flow verified. 
Co-authored-by: Cursor <cursoragent@cursor.com>
 2026-02-19 20:57:00 +08:00
HaHafeng
45c7b32dbb docs(iit): Add QC system UI and LLM format optimization plan 
- Add development plan: 07-QC system UI and LLM format optimization

- Phase 1: PromptBuilder + XML clinical slice format (~5.5h)

- Phase 2: QC cockpit + stat cards + risk heatmap (~9.5h)

- Phase 3: Variable tagging system (~5h)

- Add CRA Agent design document and prototype

- Update module status: design 100%, code 45%

- Update system status: real-time QC complete + plan ready

Co-authored-by: Cursor <cursoragent@cursor.com>
 2026-02-08 09:59:44 +08:00
HaHafeng
5db4a7064c feat(iit): Implement real-time quality control system 
Summary:

- Add 4 new database tables: iit_field_metadata, iit_qc_logs, iit_record_summary, iit_qc_project_stats

- Implement pg-boss debounce mechanism in WebhookController

- Refactor QC Worker for dual output: QC logs + record summary

- Enhance HardRuleEngine to support form-based rule filtering

- Create QcService for QC data queries

- Optimize ChatService with new intents: query_enrollment, query_qc_status

- Add admin batch operations: one-click full QC + one-click full summary

- Create IIT Admin management module: project config, QC rules, user mapping

Status: Code complete, pending end-to-end testing
Co-authored-by: Cursor <cursoragent@cursor.com>
 2026-02-07 21:56:11 +08:00
HaHafeng
0c590854b5 docs(iit): Add IIT Manager Agent V2.9 development plan with multi-agent architecture 
Features:
- Add V2.9 enhancements: Cron Skill, User Profiling, Feedback Loop, Multi-Intent Handling
- Create modular development plan documents (database, engines, services, memory, tasks)
- Add V2.5/V2.6/V2.8/V2.9 design documents for architecture evolution
- Add system design white papers and implementation guides

Architecture:
- Dual-Brain Architecture (SOP + ReAct engines)
- Three-layer memory system (Flow Log, Hot Memory, History Book)
- ProfilerService for personalized responses
- SchedulerService with Cron Skill support

Also includes:
- Frontend nginx config updates
- Backend test scripts for WeChat signature
- Database backup files

Co-authored-by: Cursor <cursoragent@cursor.com>
 2026-02-05 22:33:26 +08:00
HaHafeng
4b9b90ffb8 feat(iit): Complete REDCap production deployment on Alibaba Cloud ECS 
Summary:

- Deploy REDCap 15.8.0 on ECS with Docker CE 26.1.3

- Configure RDS MySQL 8.0 database (redcap_prod)

- Setup Nginx reverse proxy with HTTPS/SSL

- Domain configured: https://redcap.xunzhengyixue.com/

Documentation:

- Add ECS deployment guide

- Add deployment info record

- Update system status document (v4.5 -> v4.6)

Status: REDCap production environment fully operational
Co-authored-by: Cursor <cursoragent@cursor.com>
 2026-02-02 22:27:05 +08:00
HaHafeng
4c2c9b437b feat(admin): Add activity logs page and fix AI chat markdown rendering 
- Add paginated activity logs API with filters (date, module, action, keyword)

- Add ActivityLogsPage with table, filters, and detail modal

- Add markdown rendering support for AI chat messages

- Remove prototype placeholder content from chat sidebar

Co-authored-by: Cursor <cursoragent@cursor.com>
 2026-02-01 21:04:21 +08:00
HaHafeng
96290d2f76 feat(aia): Implement Protocol Agent MVP with reusable Agent framework 
Sprint 1-3 Completed (Backend + Frontend):

Backend (Sprint 1-2):
- Implement 5-layer Agent framework (Query->Planner->Executor->Tools->Reflection)
- Create agent_schema with 6 tables (agent_definitions, stages, prompts, sessions, traces, reflexion_rules)
- Create protocol_schema with 2 tables (protocol_contexts, protocol_generations)
- Implement Protocol Agent core services (Orchestrator, ContextService, PromptBuilder)
- Integrate LLM service adapter (DeepSeek/Qwen/GPT-5/Claude)
- 6 API endpoints with full authentication
- 10/10 API tests passed

Frontend (Sprint 3):
- Add Protocol Agent entry in AgentHub (indigo theme card)
- Implement ProtocolAgentPage with 3-column layout
- Collapsible sidebar (Gemini style, 48px <-> 280px)
- StatePanel with 5 stage cards (scientific_question, pico, study_design, sample_size, endpoints)
- ChatArea with sync button and action cards integration
- 100% prototype design restoration (608 lines CSS)
- Detailed endpoints structure: baseline, exposure, outcomes, confounders

Features:
- 5-stage dialogue flow for research protocol design
- Conversation-driven interaction with sync-to-protocol button
- Real-time context state management
- One-click protocol generation button (UI ready, backend pending)

Database:
- agent_schema: 6 tables for reusable Agent framework
- protocol_schema: 2 tables for Protocol Agent
- Seed data: 1 agent + 5 stages + 9 prompts + 4 reflexion rules

Code Stats:
- Backend: 13 files, 4338 lines
- Frontend: 14 files, 2071 lines
- Total: 27 files, 6409 lines

Status: MVP core functionality completed, pending frontend-backend integration testing

Next: Sprint 4 - One-click protocol generation + Word export
 2026-01-24 17:29:24 +08:00
HaHafeng
61cdc97eeb feat(platform): Fix pg-boss queue conflict and add safety standards 
Summary:
- Fix pg-boss queue conflict (duplicate key violation on queue_pkey)
- Add global error listener to prevent process crash
- Reduce connection pool from 10 to 4
- Add graceful shutdown handling (SIGTERM/SIGINT)
- Fix researchWorker recursive call bug in catch block
- Make screeningWorker idempotent using upsert

Security Standards (v1.1):
- Prohibit recursive retry in Worker catch blocks
- Prohibit payload bloat (only store fileKey/ID in job.data)
- Require Worker idempotency (upsert + unique constraint)
- Recommend task-specific expireInSeconds settings
- Document graceful shutdown pattern

New Features:
- PKB signed URL endpoint for document preview/download
- pg_bigm installation guide for Docker
- Dockerfile.postgres-with-extensions for pgvector + pg_bigm

Documentation:
- Update Postgres-Only async task processing guide (v1.1)
- Add troubleshooting SQL queries
- Update safety checklist

Tested: Local verification passed
 2026-01-23 22:07:26 +08:00
HaHafeng
9c96f75c52 feat(storage): integrate Alibaba Cloud OSS for file persistence - Add OSSAdapter and LocalAdapter with StorageFactory pattern - Integrate PKB module with OSS upload - Rename difyDocumentId to storageKey - Create 4 OSS buckets and development specification 2026-01-22 22:02:20 +08:00
HaHafeng
40c2f8e148 feat(rag): Complete RAG engine implementation with pgvector 
Major Features:
- Created ekb_schema (13th schema) with 3 tables: KB/Document/Chunk
- Implemented EmbeddingService (text-embedding-v4, 1024-dim vectors)
- Implemented ChunkService (smart Markdown chunking)
- Implemented VectorSearchService (multi-query + hybrid search)
- Implemented RerankService (qwen3-rerank)
- Integrated DeepSeek V3 QueryRewriter for cross-language search
- Python service: Added pymupdf4llm for PDF-to-Markdown conversion
- PKB: Dual-mode adapter (pgvector/dify/hybrid)

Architecture:
- Brain-Hand Model: Business layer (DeepSeek) + Engine layer (pgvector)
- Cross-language support: Chinese query matches English documents
- Small Embedding (1024) + Strong Reranker strategy

Performance:
- End-to-end latency: 2.5s
- Cost per query: 0.0025 RMB
- Accuracy improvement: +20.5% (cross-language)

Tests:
- test-embedding-service.ts: Vector embedding verified
- test-rag-e2e.ts: Full pipeline tested
- test-rerank.ts: Rerank quality validated
- test-query-rewrite.ts: Cross-language search verified
- test-pdf-ingest.ts: Real PDF document tested (Dongen 2003.pdf)

Documentation:
- Added 05-RAG-Engine-User-Guide.md
- Added 02-Document-Processing-User-Guide.md
- Updated system status documentation

Status: Production ready
 2026-01-21 20:24:29 +08:00
HaHafeng
dfc0fe0b9a feat(pkb): Integrate pgvector and create Dify replacement plan 
Summary:
- Migrate PostgreSQL to pgvector/pgvector:pg15 Docker image
- Successfully install and verify pgvector 0.8.1 extension
- Create comprehensive Dify-to-pgvector migration plan
- Update PKB module documentation with pgvector status
- Update system documentation with pgvector integration

Key changes:
- docker-compose.yml: Switch to pgvector/pgvector:pg15 image
- Add EkbDocument and EkbChunk data model design
- Design R-C-R-G hybrid retrieval architecture
- Add clinical data JSONB fields (pico, studyDesign, regimen, safety, criteria, endpoints)
- Create detailed 10-day implementation roadmap

Documentation updates:
- PKB module status: pgvector RAG infrastructure ready
- System status: pgvector 0.8.1 integrated
- New: Dify replacement development plan (01-Dify替换为pgvector开发计划.md)
- New: Enterprise medical knowledge base solution V2

Tested: PostgreSQL with pgvector verified, frontend and backend functionality confirmed
 2026-01-20 00:00:58 +08:00
HaHafeng
57fdc6ef00 feat(aia): Integrate PromptService for 10 AI agents 
Features:
- Migrate 10 agent prompts from hardcoded to database
- Add grayscale preview support (DRAFT/ACTIVE distribution)
- Implement 3-tier fallback (DB -> Cache -> Hardcoded)
- Add version management and rollback capability

Files changed:
- backend/scripts/migrate-aia-prompts.ts (new migration script)
- backend/src/common/prompt/prompt.fallbacks.ts (add AIA fallbacks)
- backend/src/modules/aia/services/agentService.ts (integrate PromptService)
- backend/src/modules/aia/services/conversationService.ts (pass userId)
- backend/src/modules/aia/types/index.ts (fix AgentStage type)

Documentation:
- docs/03-业务模块/AIA-AI智能问答/06-开发记录/2026-01-18-Prompt管理系统集成.md
- docs/02-通用能力层/00-通用能力层清单.md (add FileCard, Prompt management)
- docs/00-系统总体设计/00-系统当前状态与开发指南.md (update to v3.6)

Prompt codes:
- AIA_SCIENTIFIC_QUESTION, AIA_PICO_ANALYSIS, AIA_TOPIC_EVALUATION
- AIA_OUTCOME_DESIGN, AIA_CRF_DESIGN, AIA_SAMPLE_SIZE
- AIA_PROTOCOL_WRITING, AIA_METHODOLOGY_REVIEW
- AIA_PAPER_POLISH, AIA_PAPER_TRANSLATE

Tested: Migration script executed, all 10 prompts inserted successfully
 2026-01-18 15:48:53 +08:00
HaHafeng
66255368b7 feat(admin): Add user management and upgrade to module permission system 
Features - User Management (Phase 4.1):
- Database: Add user_modules table for fine-grained module permissions
- Database: Add 4 user permissions (view/create/edit/delete) to role_permissions
- Backend: UserService (780 lines) - CRUD with tenant isolation
- Backend: UserController + UserRoutes (648 lines) - 13 API endpoints
- Backend: Batch import users from Excel
- Frontend: UserListPage (412 lines) - list/filter/search/pagination
- Frontend: UserFormPage (341 lines) - create/edit with module config
- Frontend: UserDetailPage (393 lines) - details/tenant/module management
- Frontend: 3 modal components (592 lines) - import/assign/configure
- API: GET/POST/PUT/DELETE /api/admin/users/* endpoints

Architecture Upgrade - Module Permission System:
- Backend: Add getUserModules() method in auth.service
- Backend: Login API returns modules array in user object
- Frontend: AuthContext adds hasModule() method
- Frontend: Navigation filters modules based on user.modules
- Frontend: RouteGuard checks requiredModule instead of requiredVersion
- Frontend: Remove deprecated version-based permission system
- UX: Only show accessible modules in navigation (clean UI)
- UX: Smart redirect after login (avoid 403 for regular users)

Fixes:
- Fix UTF-8 encoding corruption in ~100 docs files
- Fix pageSize type conversion in userService (String to Number)
- Fix authUser undefined error in TopNavigation
- Fix login redirect logic with role-based access check
- Update Git commit guidelines v1.2 with UTF-8 safety rules

Database Changes:
- CREATE TABLE user_modules (user_id, tenant_id, module_code, is_enabled)
- ADD UNIQUE CONSTRAINT (user_id, tenant_id, module_code)
- INSERT 4 permissions + role assignments
- UPDATE PUBLIC tenant with 8 module subscriptions

Technical:
- Backend: 5 new files (~2400 lines)
- Frontend: 10 new files (~2500 lines)
- Docs: 1 development record + 2 status updates + 1 guideline update
- Total: ~4900 lines of code

Status: User management 100% complete, module permission system operational
 2026-01-16 13:42:10 +08:00
HaHafeng
3d35e9c58b feat(aia): Complete AIA V2.0 with universal streaming capabilities 
Major Updates:
- Add StreamingService with OpenAI Compatible format (backend/common/streaming)
- Upgrade Chat component V2 with Ant Design X integration
- Implement AIA module with 12 intelligent agents
- Create AgentHub with 100% prototype V11 restoration
- Create ChatWorkspace with streaming response support
- Add ThinkingBlock for deep thinking display
- Add useAIStream Hook for OpenAI Compatible stream handling

Backend Common Capabilities (~400 lines):
- OpenAIStreamAdapter: SSE adapter with OpenAI format
- StreamingService: unified streaming service
- Support content and reasoning_content dual streams
- Deep thinking tag processing (<think>...</think>)

Frontend Common Capabilities (~2000 lines):
- AIStreamChat: modern streaming chat component
- ThinkingBlock: collapsible deep thinking display
- ConversationList: conversation management with grouping
- useAIStream: OpenAI Compatible stream handler Hook
- useConversations: conversation state management Hook
- Modern design styles (Ultramodern theme)

AIA Module Frontend (~1500 lines):
- AgentHub: 12 agent cards with timeline design
- ChatWorkspace: fullscreen immersive chat interface
- AgentCard: theme-colored cards (blue/yellow/teal/purple)
- 5 phases, 12 agents configuration
- Responsive layout (desktop + mobile)

AIA Module Backend (~900 lines):
- agentService: 12 agents config with system prompts
- conversationService: refactored with StreamingService
- attachmentService: file upload skeleton (30k token limit)
- 12 API endpoints with authentication
- Full CRUD for conversations and messages

Documentation:
- AIA module status and development guide
- Universal capabilities catalog (11 services)
- Quick reference card for developers
- System overview updates

Testing:
- Stream response verified (HTTP 200)
- Authentication working correctly
- Auto conversation creation working
- Deep thinking display working
- Message input and send working

Status: Core features completed (85%), attachment and history loading pending
 2026-01-14 19:09:28 +08:00