69 Commits

Author SHA1 Message Date
c3554fd61d feat(rvw): harden json parsing and finalize 0316 rollout
Stabilize RVW editorial and methodology JSON parsing in production with layered repair and fallback handling, then publish the paired frontend task-level language selector updates. Also reset deployment checklist, record the 0316 deployment summary, and refresh the SAE runtime status with latest backend/frontend IPs.

Made-with: Cursor
2026-03-16 00:24:33 +08:00
707f783229 feat(rvw): complete tenant portal polish and ops assignment fixes
Finalize RVW tenant portal UX and reliability updates by aligning login/profile interactions, stabilizing SMS code sends in weak-network scenarios, and fixing multi-tenant assignment payload handling to prevent runtime errors. Refresh RVW status and deployment checklist docs with SAE routing, frontend image build, and post-release validation guidance.

Made-with: Cursor
2026-03-15 18:22:01 +08:00
83e395824b feat(rvw): complete journal config center MVP and tenant login routing
Deliver the RVW V4.0 journal configuration center across backend, frontend, migration, and docs with zh/en editorial baseline support and tenant-level prompt/template overrides. Unify tenant login to /:tenantCode/login and auto-enable RVW module when tenant type is JOURNAL to prevent post-login access gaps.

Made-with: Cursor
2026-03-15 11:51:35 +08:00
16179e16ca feat(rvw): deliver tenant portal v4 flow and config foundation
Implement RVW V4.0 tenant-aware backend/frontend flow with tenant routing, config APIs, and full portal UX updates. Sync system/RVW/deployment docs to capture verified upload-review-report workflow and next-step admin configuration work.

Made-with: Cursor
2026-03-14 22:29:40 +08:00
ba464082cb feat(core): finalize rvw stability updates and pending module changes
Summary:
- Harden RVW prompt protocol handling and methodology review flow with 20-checkpoint coverage, divide-and-conquer execution, and timeout tuning
- Update RVW frontend methodology report rendering to show real structured outputs and grouped checkpoint sections
- Include pending backend/frontend updates across IIT admin, SSA, extraction forensics, and related integration files
- Sync system and RVW status documentation, deployment checklist, and RVW architecture/plan docs

Validation:
- Verified lint diagnostics for touched RVW backend/frontend files show no new errors
- Kept backup dump files and local test artifacts untracked

Made-with: Cursor
2026-03-14 00:00:04 +08:00
6edfad032f feat(ssa): finalize strict stepwise agent execution flow
Align Agent mode to strict stepwise generation and execution, add deterministic and safety hardening, and sync deployment/module documentation for Phase 5A.5/5B/5C rollout.

- implement strict stepwise execution path and dependency short-circuiting
- persist step-level errors/results and stream step_* progress events
- add agent plan params patch route and schema/migration support
- improve R sanitizer/security checks and step result rendering in workspace
- update SSA module guide and deployment change checklist

Made-with: Cursor
2026-03-11 22:49:05 +08:00
d3b24bd8c3 chore(deploy): record 0310 rollout and reset checklist
Update deployment documents for the 0310 SAE release, including new backend/frontend service IPs, latest image versions, and a fresh 0310 deployment summary. Also reset the pending deployment checklist after successful rollout and include the ASL navigation toggle adjustment.

Made-with: Cursor
2026-03-10 22:26:06 +08:00
08108e81cd fix(ssa): harden spreadsheet upload recognition and guidance
Fix SSA data-context generation for Excel uploads by parsing xlsx/xls via extension-aware paths instead of UTF-8 fallback.
Add on-demand overview rebuild in Agent flow, align xls friendly prompts on frontend/backend, and surface backend upload errors to users.

Made-with: Cursor
2026-03-10 21:37:34 +08:00
d96cdf3fe8 fix(aia): stabilize attachment parsing and expand spreadsheet support
Align AIA attachment handling with actual extractor capability by adding xlsx/csv gray support, guiding doc/xls users to convert formats, and enforcing attachment-only answering to prevent system knowledge leakage.

Made-with: Cursor
2026-03-10 13:15:36 +08:00
097e7920ab feat(admin): add user-level direct permission system and enhance activity tracking
Features:
- Add user_permissions table for direct user-to-permission grants (ops:user-ops)
- Merge role_permissions + user_permissions in auth chain (login, middleware, getCurrentUser)
- Add getUserQueryScope support for USER role with ops:user-ops (cross-tenant access)
- Unify cross-tenant operation checks via getUserQueryScope (remove hardcoded SUPER_ADMIN checks)
- Add 3 new API endpoints: GET/PUT /:id/permissions, GET /options/permissions
- Support ops:user-ops as alternative permission on all user/tenant management routes
- Frontend: add user-ops permission toggle on UserFormPage and UserDetailPage
- Enhance DC module activity tracking (StreamAIController, SessionController, QuickActionController)
- Fix DC AIController user ID extraction and feature name consistency
- Add verify-activity-tracking.ts validation script
- Update deployment checklist and admin module documentation

DB Migration: 20260309_add_user_permissions_table

Made-with: Cursor
2026-03-10 09:02:35 +08:00
971e903acf chore(deploy): finalize 0309 SAE rollout updates
Sync deployment documentation to the final successful SAE state and clear pending deployment checklist items. Include backend/frontend/R hardening and diagnostics improvements required for stable production behavior.

Made-with: Cursor
2026-03-09 22:27:11 +08:00
d30bf95815 feat(auth): integrate Aliyun SMS verification flow with docs update
Wire auth verification-code delivery to Aliyun SMS with mock fallback, config validation, and a standalone SMS smoke-test script. Update deployment checklist and system status docs with required env vars and rollout notes.

Made-with: Cursor
2026-03-09 20:30:52 +08:00
5c5fec52c1 fix(aia,ssa,asl,infra): harden SSE transport and stabilize attachment context
Deliver SSE protocol hardening for SAE/HTTP2 paths, add graceful shutdown health behavior, and improve SSA retry UX for transient stream failures. For AIA, persist attachment extraction results in database with cache read-through fallback, plus production cache safety guard to prevent memory-cache drift in multi-instance deployments; also restore ASL SR page scrolling behavior.

Made-with: Cursor
2026-03-09 18:45:12 +08:00
50657dd81f fix(auth): enforce single-session with DB tokenVersion + heartbeat detection
Move single-session invalidation from cache-based token version checks to a database-backed, atomic tokenVersion flow to eliminate concurrent login race conditions. Add a global auth heartbeat (visibility-aware) so kicked sessions are detected within ~10s when the page is visible.

Made-with: Cursor
2026-03-09 13:11:37 +08:00
a666649fd4 feat(iit): harden QC pipeline consistency and release artifacts
Implement IIT quality workflow hardening across eQuery deduplication, guard metadata validation, timeline/readability improvements, and chat evidence fallbacks, then synchronize release and development documentation for deployment handoff.

Includes migration/scripts for open eQuery dedupe guards, orchestration/status semantics, report/tool readability fixes, and updated module status plus deployment checklist.

Made-with: Cursor
2026-03-08 21:54:35 +08:00
ac724266c1 feat(ssa): SSA Agent mode MVP - prompt management + Phase 5A guardrails + UX enhancements
Backend:
- Agent core prompts (Planner + Coder) now loaded from PromptService with 3-tier fallback (DB -> cache -> hardcoded)
- Seed script (seed-ssa-agent-prompts.ts) for idempotent SSA_AGENT_PLANNER + SSA_AGENT_CODER setup
- SSA fallback prompts added to prompt.fallbacks.ts
- Phase 5A: XML tag extraction, defensive programming prompt, high-fidelity schema injection, AST pre-check
- Default agent mode migration + session CRUD (rename/delete) APIs
- R Docker: structured error handling (20+ patterns) + AST syntax pre-check

Frontend:
- Default agent mode (QPER toggle removed), view code fix, analysis result cards in chat
- Session history sidebar with inline rename/delete, robust plan parsing from reviewResult
- R code export wrapper for local reproducibility (package checks + data loader + polyfills)
- SSA workspace CSS updates for sidebar actions and plan display

Docs:
- SSA module doc v4.2: Prompt inventory (2 Agent active / 11 QPER archived), dev progress updated
- System overview doc v6.8: SSA Agent MVP milestone
- Deployment checklist: DB-5 (seed script) + BE-10 (prompt management)

Made-with: Cursor
2026-03-08 15:23:09 +08:00
52989cd03f feat(ssa): Agent channel UX optimization (Solution B) + Plan-and-Execute architecture design
SSA Agent channel improvements (12 code files, +931/-203 lines):
- Solution B: left/right separation of concerns (gaze guiding + state mutex + time-travel)
- JWT token refresh mechanism (ensureFreshToken) to fix HTTP 401 during pipeline
- Code truncation fix: LLM maxTokens 4000->8000 + CSS max-height 60vh
- Retry streaming code generation with generateCodeStream()
- R Docker structured errors: 20+ pattern matching + format_agent_error + line extraction
- Prompt iron rules: strict output format in CoderAgent System Prompt
- parseCode robustness: XML/Markdown/inference 3-tier matching + length validation
- consoleOutput type defense: handle both array and scalar from R Docker unboxedJSON
- Agent progress bar sync: derive phase from agentExecution.status
- Export report / view code buttons restored for Agent mode
- ExecutingProgress component: real-time timer + dynamic tips + step pulse animation

Architecture design (3 review reports):
- Plan-and-Execute step-by-step execution architecture approved
- Code accumulation strategy (R Docker stays stateless)
- 5 engineering guardrails: XML tags, AST pre-check, defensive prompts, high-fidelity schema, error classification circuit breaker

Docs: update SSA module status v4.1, system status v6.7, deployment changelist
Made-with: Cursor
2026-03-07 22:32:32 +08:00
87655ea7e6 feat(rvw,asl): RVW V3.0 smart review + ASL deep research history + stability
RVW module (V3.0 Smart Review Enhancement):
- Add LLM data validation via PromptService (RVW_DATA_VALIDATION)
- Add ClinicalAssessmentSkill with FINER-based evaluation (RVW_CLINICAL)
- Remove all numeric scores from UI (editorial, methodology, overall)
- Implement partial_completed status with Promise.allSettled
- Add error_details JSON field to ReviewTask for granular failure info
- Fix overallStatus logic: warning status now counts as success
- Restructure ForensicsReport: per-table LLM results, remove top-level block
- Refactor ClinicalReport: structured collapsible sections
- Increase all skill timeouts to 300s for long manuscripts (20+ pages)
- Increase DataForensics LLM timeout to 180s, pg-boss to 15min
- Executor default fallback timeout 30s -> 60s

ASL module:
- Add deep research history with sidebar accordion UI
- Implement waterfall flow for historical task display
- Upgrade Unifuncs DeepSearch API from S2 to S3 with fallback
- Add ASL_SR module seed for admin configurability
- Fix new search button inconsistency

Docs:
- Update RVW module status to V3.0
- Update deployment changelist
- Add 0305 deployment summary

DB Migration:
- Add error_details JSONB column to rvw_schema.review_tasks

Tested: All 4 review modules verified, partial completion working
Made-with: Cursor
2026-03-07 19:24:21 +08:00
91ae80888e feat(admin,rvw,asl,frontend): Batch import redesign + RVW parallel skills + UI improvements
Backend:
- Redesign batch user import: add autoInheritModules param, users auto-inherit tenant modules when true
- Add module validation: reject modules not subscribed by the tenant
- Soften department validation: skip instead of fail when department name not found
- Fix RVW skill status semantics: review findings (ERROR issues) no longer mark skill as error
- Add parallel execution support to SkillExecutor via parallelGroup
- Configure Editorial + Methodology skills to run in parallel (~240s -> ~130s)
- Update legacy bridge error message to user-friendly text

Frontend:
- Redesign ImportUserModal: 4-step flow (select tenant -> upload -> preview -> result)
- Simplify import template: remove tenant code and module columns
- Show tenant subscribed modules before import with auto-inherit option
- Fix isLegacyEmbed modules bypassing RouteGuard and TopNavigation permission checks
- Hide ASL fulltext screening (step 3), renumber subsequent nav items
- Add ExtractionWorkbenchGuide page when no taskId provided
- Update legacy system error message to network-friendly text

Docs:
- Update deployment changelog with BE-9, FE-11 entries

Made-with: Cursor
2026-03-05 22:04:36 +08:00
aadceb5cde feat(ssa): Implement dual-channel architecture Phase 1-3 (QPER + LLM Agent pipeline)
Completed:
- Phase 1: DB schema (execution_mode + ssa_agent_executions), ModeToggle component, Session PATCH API
- Phase 2: AgentPlannerService + AgentCoderService (streaming) + CodeRunnerService + R Docker /execute-code endpoint
- Phase 3: AgentCodePanel (3-step confirmation UI), SSE event handling (7 agent events), streaming code display
- Three-step confirmation pipeline: plan -> user confirm -> stream code -> user confirm -> execute R code -> results
- R Docker sandbox /execute-code endpoint with 120s timeout + block_helpers preloaded
- E2E dual-channel test script (8 tests)
- Updated R engine architecture doc (v1.5) and SSA module status doc (v4.0)

Technical details:
- AgentCoderService uses LLM streaming (chatStream) for real-time code generation feedback
- ReviewerAgent temporarily disabled, prioritizing Plan -> Code -> Execute flow
- CodeRunnerService wraps user code with auto data loading (df variable injection)
- Frontend handles agent_planning, agent_plan_ready, code_generating, code_generated, code_executing, code_result events
- ask_user mechanism used for plan and code confirmation steps

Files: 24 files (4 new services, 2 new components, 1 migration, 1 E2E test, 16 modified)
Made-with: Cursor
2026-03-02 22:23:54 +08:00
71d32d11ee feat(iit): V3.2 data consistency + project isolation + admin config redesign + Chinese labels
Summary:
- Refactor timeline API to read from qc_field_status (SSOT) instead of qc_logs
- Add field-issues paginated API with severity/dimension/recordId filters
- Add LEFT JOIN field_metadata + qc_event_status for Chinese display names
- Implement per-project ChatOrchestrator cache and SessionMemory isolation
- Redesign admin IIT config tabs (REDCap -> Fields -> KB -> Rules -> Members)
- Add AI-powered QC rule generation (D3 programmatic + D1/D5/D6 LLM-based)
- Add clickable warning/critical detail Modal in ReportsPage
- Auto-dispatch eQuery after batch QC via DailyQcOrchestrator
- Update module status documentation to v3.2

Backend changes:
- iitQcCockpitController: rewrite getTimeline from qc_field_status, add getFieldIssues
- iitQcCockpitRoutes: add field-issues route
- ChatOrchestrator: per-projectId cached instances
- SessionMemory: keyed by userId::projectId
- WechatCallbackController: resolve projectId from iitUserMapping
- iitRuleSuggestionService: dimension-based suggest + generateD3Rules
- iitBatchController: call DailyQcOrchestrator after batch QC

Frontend changes:
- AiStreamPage: adapt to new timeline structure with dimension tags
- ReportsPage: clickable stats cards with issue detail Modal
- IitProjectDetailPage: reorder tabs, add AI rule generation UI
- iitProjectApi: add TimelineIssue, FieldIssueItem types and APIs

Status: TypeScript compilation verified, no new lint errors
Made-with: Cursor
2026-03-02 14:29:59 +08:00
72928d3116 docs(deploy): Complete 0302 deployment documentation for IIT V3.1 QC engine upgrade
Summary:
- Create 0302 deployment summary (6 DB migrations + backend v2.4 + frontend v2.0)
- Update SAE status record with new IPs (172.17.197.32), versions, and history
- Update daily operations manual with incremented version numbers (backend v2.5, frontend v2.1)
- Clear pending deployment checklist and archive to history section
- Fix stale schema table counts (iit_schema 5->22, ssa_schema 0->11)

Deployment details:
- Database: 6 Prisma migrations applied (84->86 tables, 442 columns verified identical)
- Backend: v2.3->v2.4 (27 changes, IIT V3.1 QC engine + GCP report APIs)
- Frontend: v1.9->v2.0 (17 changes, GCP 5-tab reports + V3.1 dashboard)
- Both services deployed to SAE at 172.17.197.32

Made-with: Cursor
2026-03-02 08:36:56 +08:00
2030ebe28f feat(iit): Complete V3.1 QC engine + GCP business reports + AI timeline + bug fixes
V3.1 QC Engine:
- QcExecutor unified entry + D1-D7 dimension engines + three-level aggregation
- HealthScoreEngine + CompletenessEngine + ProtocolDeviationEngine + QcAggregator
- B4 flexible cron scheduling (project-level cronExpression + pg-boss dispatcher)
- Prisma migrations for qc_field_status, event_status, project_stats

GCP Business Reports (Phase A - 4 reports):
- D1 Eligibility: record_summary full list + qc_field_status D1 overlay
- D2 Completeness: data entry rate and missing rate aggregation
- D3/D4 Query Tracking: severity distribution from qc_field_status
- D6 Protocol Deviation: D6 dimension filtering
- 4 frontend table components + ReportsPage 5-tab restructure

AI Timeline Enhancement:
- SkillRunner outputs totalRules (33 actual rules vs 1 skill)
- iitQcCockpitController severity mapping fix (critical->red, warning->yellow)
- AiStreamPage expandable issue detail table with Chinese labels
- Event label localization (eventLabel from backend)

Business-side One-click Batch QC:
- DashboardPage batch QC button with SyncOutlined icon
- Auto-refresh QcReport cache after batch execution

Bug Fixes:
- dimension_code -> rule_category in 4 SQL queries
- D1 eligibility data source: record_summary full + qc_field_status overlay
- Timezone UTC -> Asia/Shanghai (QcReportService toBeijingTime helper)
- Pass rate calculation: passed/totalEvents instead of passed/totalRecords

Docs:
- Update IIT module status with GCP reports and bug fix milestones
- Update system status doc v6.6 with IIT progress

Tested: Backend compiles, frontend linter clean, batch QC verified
Made-with: Cursor
2026-03-01 22:49:49 +08:00
0b29fe88b5 feat(iit): QC deep fix + V3.1 architecture plan + project member management
QC System Deep Fix:
- HardRuleEngine: add null tolerance + field availability pre-check (skipped status)
- SkillRunner: baseline data merge for follow-up events + field availability check
- QcReportService: record-level pass rate calculation + accurate LLM XML report
- iitBatchController: legacy log cleanup (eventId=null) + upsert RecordSummary
- seed-iit-qc-rules: null/empty string tolerance + applicableEvents config

V3.1 Architecture Design (docs only, no code changes):
- QC engine V3.1 plan: 5-level data structure (CDISC ODM) + D1-D7 dimensions
- Three-batch implementation strategy (A: foundation, B: bubbling, C: new engines)
- Architecture team review: 4 whitepapers reviewed + feedback doc + 4 critical suggestions
- CRA Agent strategy roadmap + CRA 4-tool explanation doc for clinical experts

Project Member Management:
- Cross-tenant member search and assignment (remove tenant restriction)
- IIT project detail page enhancement with tabbed layout (KB + members)
- IitProjectContext for business-side project selection
- System-KB route access control adjustment for project operators

Frontend:
- AdminLayout sidebar menu restructure
- IitLayout with project context provider
- IitMemberManagePage new component
- Business-side pages adapt to project context

Prisma:
- 2 new migrations (user-project RBAC + is_demo flag)
- Schema updates for project member management

Made-with: Cursor
2026-03-01 15:27:05 +08:00
6124c7abc6 docs(platform): Add database documentation system and restructure deployment docs
Completed:
- Add 6 core database documents (docs/01-平台基础层/07-数据库/)
  Architecture overview, migration history, environment comparison,
  tech debt tracking, seed data management, PostgreSQL extensions
- Restructure deployment docs: archive 20 legacy files to _archive-2025/
- Create unified daily operations manual (01-日常更新操作手册.md)
- Add pending deployment change tracker (03-待部署变更清单.md)
- Update database development standard to v3.0 (three iron rules)
- Fix Prisma schema type drift: align @db.* annotations with actual DB
  IIT: UUID/Timestamptz(6), SSA: Timestamp(6)/VarChar(20/50/100)
- Add migration: 20260227_align_schema_with_db_types (idempotent ALTER)
- Add Cursor Rule for auto-reminding deployment change documentation
- Update system status guide v6.4 with deployment and DB doc references
- Add architecture consultation docs (Prisma guide, SAE deployment guide)

Technical details:
- Manual migration due to shadow DB limitation (TD-001 in tech debt)
- Deployment docs reduced from 20+ scattered files to 3 core documents
- Cursor Rule triggers on schema.prisma, package.json, Dockerfile changes

Made-with: Cursor
2026-02-27 14:35:25 +08:00
bbf98c4d5c fix(backend): Resolve PgBoss infinite loop issue and cleanup unused files
Backend fixes:
- Fix PgBoss task infinite loop on SAE (root cause: missing queue table constraints)
- Add singletonKey to prevent duplicate job enqueueing
- Add idempotency check in reviewWorker (skip completed tasks)
- Add optimistic locking in reviewService (atomic status update)

Frontend fixes:
- Add isSubmitting state to prevent duplicate submissions in RVW Dashboard
- Fix API baseURL in knowledgeBaseApi (relative path)

Cleanup (removed):
- Old frontend/ directory (migrated to frontend-v2)
- python-microservice/ (unused, replaced by extraction_service)
- Root package.json and node_modules (accidentally created)
- redcap-docker-dev/ (external dependency)
- Various temporary files and outdated docs in root

New documentation:
- docs/07-运维文档/01-PgBoss队列监控与维护.md
- docs/07-运维文档/02-故障预防检查清单.md
- docs/07-运维文档/03-数据库迁移注意事项.md

Database fix applied to RDS:
- Added PRIMARY KEY to platform_schema.queue
- Added 3 missing foreign key constraints

Tested: Local build passed, RDS constraints verified
2026-01-27 18:16:22 +08:00
2481b786d8 deploy: Complete 0126-27 deployment - database upgrade, services update, code recovery
Major Changes:
- Database: Install pg_bigm/pgvector plugins, create test database
- Python service: v1.0 -> v1.1, add pymupdf4llm/openpyxl/pypandoc
- Node.js backend: v1.3 -> v1.7, fix pino-pretty and ES Module imports
- Frontend: v1.2 -> v1.3, skip TypeScript check for deployment
- Code recovery: Restore empty files from local backup

Technical Fixes:
- Fix pino-pretty error in production (conditional loading)
- Fix ES Module import paths (add .js extensions)
- Fix OSSAdapter TypeScript errors
- Update Prisma Schema (63 models, 16 schemas)
- Update environment variables (DATABASE_URL, EXTRACTION_SERVICE_URL, OSS)
- Remove deprecated variables (REDIS_URL, DIFY_API_URL, DIFY_API_KEY)

Documentation:
- Create 0126 deployment folder with 8 documents
- Update database development standards v2.0
- Update SAE deployment status records

Deployment Status:
- PostgreSQL: ai_clinical_research_test with plugins
- Python: v1.1 @ 172.17.173.84:8000
- Backend: v1.7 @ 172.17.173.89:3001
- Frontend: v1.3 @ 172.17.173.90:80

Tested: All services running successfully on SAE
2026-01-27 08:13:27 +08:00
303dd78c54 feat(aia): Protocol Agent MVP complete with one-click generation and Word export
- Add one-click research protocol generation with streaming output

- Implement Word document export via Pandoc integration

- Add dynamic dual-panel layout with resizable split pane

- Implement collapsible content for StatePanel stages

- Add conversation history management with title auto-update

- Fix scroll behavior, markdown rendering, and UI layout issues

- Simplify conversation creation logic for reliability
2026-01-25 19:16:36 +08:00
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
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
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
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
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
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
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
1b53ab9d52 feat(aia): Complete AIA V2.0 with universal streaming capabilities
Major Changes:
- Add StreamingService with OpenAI Compatible format
- Upgrade Chat component V2 with Ant Design X integration
- Implement AIA module with 12 intelligent agents
- Update API routes to unified /api/v1 prefix
- Update system documentation

Backend (~1300 lines):
- common/streaming: OpenAI Compatible adapter
- modules/aia: 12 agents, conversation service, streaming integration
- Update route versions (RVW, PKB to v1)

Frontend (~3500 lines):
- modules/aia: AgentHub + ChatWorkspace (100% prototype restoration)
- shared/Chat: AIStreamChat, ThinkingBlock, useAIStream Hook
- Update API endpoints to v1

Documentation:
- AIA module status guide
- Universal capabilities catalog
- System overview updates
- All module documentation sync

Tested: Stream response verified, authentication working
Status: AIA V2.0 core completed (85%)
2026-01-14 19:15:01 +08:00
4ed67a8846 fix(admin): Fix Prompt management list not showing version info and add debug diagnostics
Summary:
- Fix Prompt list API response schema missing activeVersion and draftVersion fields
- Fastify was filtering out undefined schema fields, causing version columns to show empty
- Add detailed diagnostic logging for Prompt debug mode troubleshooting
- Verify debug mode works correctly (DRAFT version is used when debug enabled)

Changes:
- backend/src/common/prompt/prompt.routes.ts: Add activeVersion and draftVersion to response schema
- backend/src/common/prompt/prompt.service.ts: Add diagnostic logs for setDebugMode and get methods
- PKB module: Various authentication and document handling fixes from previous session

Tested: Debug mode verified working - v2 DRAFT version correctly loaded when debug enabled
2026-01-13 22:22:10 +08:00
4088275290 fix(pkb): fix create KB and upload issues - remove simulated upload, fix department mapping, add upload modal
Fixed issues:
- Remove simulateUpload function from DashboardPage Step 3
- Map department to description field when creating KB
- Add upload modal in WorkspacePage knowledge assets tab
- Fix DocumentUpload import path (../../stores to ../stores)

Known issue: Dify API validation error during document upload (file uploaded but DB record failed, needs investigation)

Testing: KB creation works, upload dialog opens correctly
2026-01-13 13:17:20 +08:00
5523ef36ea feat(admin): Complete Phase 3.5.1-3.5.4 Prompt Management System (83%)
Summary:
- Implement Prompt management infrastructure and core services
- Build admin portal frontend with light theme
- Integrate CodeMirror 6 editor for non-technical users

Phase 3.5.1: Infrastructure Setup
- Create capability_schema for Prompt storage
- Add prompt_templates and prompt_versions tables
- Add prompt:view/edit/debug/publish permissions
- Migrate RVW prompts to database (RVW_EDITORIAL, RVW_METHODOLOGY)

Phase 3.5.2: PromptService Core
- Implement gray preview logic (DRAFT for debuggers, ACTIVE for users)
- Module-level debug control (setDebugMode)
- Handlebars template rendering
- Variable extraction and validation (extractVariables, validateVariables)
- Three-level disaster recovery (database -> cache -> hardcoded fallback)

Phase 3.5.3: Management API
- 8 RESTful endpoints (/api/admin/prompts/*)
- Permission control (PROMPT_ENGINEER can edit, SUPER_ADMIN can publish)

Phase 3.5.4: Frontend Management UI
- Build admin portal architecture (AdminLayout, OrgLayout)
- Add route system (/admin/*, /org/*)
- Implement PromptListPage (filter, search, debug switch)
- Implement PromptEditor (CodeMirror 6 simplified for clinical users)
- Implement PromptEditorPage (edit, save, publish, test, version history)

Technical Details:
- Backend: 6 files, ~2044 lines (prompt.service.ts 596 lines)
- Frontend: 9 files, ~1735 lines (PromptEditorPage.tsx 399 lines)
- CodeMirror 6: Line numbers, auto-wrap, variable highlight, search, undo/redo
- Chinese-friendly: 15px font, 1.8 line-height, system fonts

Next Step: Phase 3.5.5 - Integrate RVW module with PromptService

Tested: Backend API tests passed (8/8), Frontend pending user testing
Status: Ready for Phase 3.5.5 RVW integration
2026-01-11 21:25:16 +08:00
440f75255e feat(rvw): Complete Phase 4-5 - Bug fixes and Word export
Summary:
- Fix methodology score display issue in task list (show score instead of 'warn')
- Add methodology_score field to database schema
- Fix report display when only methodology agent is selected
- Implement Word document export using docx library
- Update documentation to v3.0/v3.1

Backend changes:
- Add methodologyScore to Prisma schema and TaskSummary type
- Update reviewWorker to save methodologyScore
- Update getTaskList to return methodologyScore

Frontend changes:
- Install docx and file-saver libraries
- Implement handleExportReport with Word generation
- Fix activeTab auto-selection based on available data
- Add proper imports for docx components

Documentation:
- Update RVW module status to 90% (Phase 1-5 complete)
- Update system status document to v3.0

Tested: All review workflows verified, Word export functional
2026-01-10 22:52:15 +08:00
179afa2c6b feat(rvw): Complete RVW module development Phase 1-3
Summary:
- Migrate backend to modules/rvw with v2 API routes (/api/v2/rvw)
- Add new database fields: selectedAgents, editorialScore, methodologyStatus, picoExtract, isArchived
- Create frontend module in frontend-v2/src/modules/rvw
- Implement Dashboard with task list, filtering, batch operations
- Implement ReportDetail with dual tabs (editorial/methodology)
- Implement AgentModal for intelligent agent selection
- Register RVW module in moduleRegistry.ts
- Add navigation entry in TopNavigation
- Update documentation for RVW module status (v3.0)
- Update system status document (v2.9)

Features:
- User can select agents: editorial, methodology, or both
- Support batch task execution
- Task status filtering
- Replace console.log with logger service
- Maintain v1 API backward compatibility

Tested: Frontend and backend verified locally
Status: 85% complete (Phase 1-3 done)
2026-01-07 22:39:08 +08:00
06028c6952 feat(pkb): implement complete batch processing workflow and frontend optimization
- Frontend V3 architecture migration to modules/pkb
- Implement three work modes: full-text reading, deep reading, batch processing
- Complete batch processing: template selection, progress display, result export (CSV)
- Integrate Ant Design X Chat component with streaming support
- Add document upload modal with drag-and-drop support
- Optimize UI: multi-line table display, citation formatting, auto-scroll
- Fix 10+ technical issues: API mapping, state sync, form clearing
- Update documentation: development records and module status

Performance: 3 docs batch processing ~17-28s
Status: PKB module now production-ready (90% complete)
2026-01-07 18:23:43 +08:00
e59676342a docs(pkb): Add development records and update system status
Summary:
- Add PKB module development record for 2026-01-07
- Create PKB module status document (00-模块当前状态与开发指南.md)
- Update system status document to v2.7

Documents added:
- docs/03-业务模块/PKB-个人知识库/06-开发记录/2026-01-07_PKB模块前端V3设计实现.md
- docs/03-业务模块/PKB-个人知识库/00-模块当前状态与开发指南.md

Documents updated:
- docs/00-系统总体设计/00-系统当前状态与开发指南.md

PKB module progress: 75% complete
- Frontend Dashboard: 90%
- Frontend Workspace: 85%
- 3 work modes implemented
- Batch processing API pending debug
2026-01-07 10:35:03 +08:00
5a17d096a7 feat(pkb): Complete PKB module frontend migration with V3 design
Summary:
- Implement PKB Dashboard and Workspace pages based on V3 prototype
- Add single-layer header with integrated Tab navigation
- Implement 3 work modes: Full Text, Deep Read, Batch Processing
- Integrate Ant Design X Chat component for AI conversations
- Create BatchModeComplete with template selection and document processing
- Add compact work mode selector with dropdown design

Backend:
- Migrate PKB controllers and services to /modules/pkb structure
- Register v2 API routes at /api/v2/pkb/knowledge
- Maintain dual API routes for backward compatibility

Technical details:
- Use Zustand for state management
- Handle SSE streaming responses for AI chat
- Support document selection for Deep Read mode
- Implement batch processing with progress tracking

Known issues:
- Batch processing API integration pending
- Knowledge assets page navigation needs optimization

Status: Frontend functional, pending refinement
2026-01-06 22:15:42 +08:00
b31255031e feat(iit-manager): Add WeChat Official Account integration for patient notifications
Features:
- PatientWechatCallbackController for URL verification and message handling
- PatientWechatService for template and customer messages
- Support for secure mode (message encryption/decryption)
- Simplified route /wechat/patient/callback for WeChat config
- Event handlers for subscribe/unsubscribe/text messages
- Template message for visit reminders

Technical details:
- Reuse @wecom/crypto for encryption (compatible with Official Account)
- Relaxed Fastify schema validation to prevent early request blocking
- Access token caching (7000s with 5min pre-refresh)
- Comprehensive logging for debugging

Testing: Local URL verification passed, ready for SAE deployment

Status: Code complete, waiting for WeChat platform configuration
2026-01-04 22:53:42 +08:00
dfc472810b feat(iit-manager): Integrate Dify knowledge base for hybrid retrieval
Completed features:
- Created Dify dataset (Dify_test0102) with 2 processed documents
- Linked test0102 project with Dify dataset ID
- Extended intent detection to recognize query_protocol intent
- Implemented queryDifyKnowledge method (semantic search Top 5)
- Integrated hybrid retrieval (REDCap data + Dify documents)
- Fixed AI hallucination bugs (intent detection + API field path)
- Developed debugging scripts
- Completed end-to-end testing (5 scenarios passed)
- Generated comprehensive documentation (600+ lines)
- Updated development plans and module status

Technical highlights:
- Single project single knowledge base architecture
- Smart routing based on user intent
- Prevent AI hallucination by injecting real data/documents
- Session memory for multi-turn conversations
- Reused LLMFactory for DeepSeek-V3 integration

Bug fixes:
- Fixed intent detection missing keywords
- Fixed Dify API response field path error

Testing: All scenarios verified in WeChat production environment

Status: Fully tested and deployed
2026-01-04 15:44:11 +08:00
b47079b387 feat(iit): Phase 1.5 AI对话集成REDCap真实数据完成
- feat: ChatService集成DeepSeek-V3实现AI对话(390行)
- feat: SessionMemory实现上下文记忆(最近3轮对话,170行)
- feat: 意图识别支持REDCap数据查询(关键词匹配)
- feat: REDCap数据注入LLM(queryRedcapRecord, countRedcapRecords, getProjectInfo)
- feat: 解决LLM幻觉问题(基于真实数据回答,明确system prompt)
- feat: 即时反馈(正在查询...提示)
- test: REDCap查询测试通过(test0102项目,10条记录,ID 7患者详情)
- docs: 创建Phase1.5开发完成记录(313行)
- docs: 更新Phase1.5开发计划(标记完成)
- docs: 更新MVP开发任务清单(Phase 1.5完成)
- docs: 更新模块当前状态(60%完成度)
- docs: 更新系统总体设计文档(v2.6)
- chore: 删除测试脚本(test-redcap-query-for-ai.ts, check-env-config.ts)
- chore: 移除REDCap测试环境变量(REDCAP_TEST_*)

技术亮点:
- AI基于REDCap真实数据对话,不编造信息
- 从数据库读取项目配置,不使用环境变量
- 企业微信端测试通过,用户体验良好

测试通过:
-  查询项目记录总数(10条)
-  查询特定患者详情(ID 7)
-  项目信息查询
-  上下文记忆(3轮对话)
-  即时反馈提示

影响范围:IIT Manager Agent模块
2026-01-03 22:48:10 +08:00
5f089516cb feat(iit-manager): Day 3 企业微信集成开发完成
- 新增WechatService(企业微信推送服务,支持文本/卡片/Markdown消息)
- 新增WechatCallbackController(异步回复模式,5秒内响应)
- 完善iit_quality_check Worker(调用WechatService推送通知)
- 新增企业微信回调路由(GET验证+POST接收消息)
- 实现LLM意图识别(query_weekly_summary/query_patient_info等)
- 安装依赖:@wecom/crypto, xml2js
- 更新开发记录文档和MVP开发计划

技术要点:
- 使用异步回复模式规避企业微信5秒超时限制
- 使用@wecom/crypto官方库处理XML加解密
- 使用setImmediate实现后台异步处理
- 支持主动推送消息返回LLM处理结果
- 完善审计日志记录(WECHAT_NOTIFICATION_SENT/WECHAT_INTERACTION)

相关文档:
- docs/03-业务模块/IIT Manager Agent/06-开发记录/Day3-企业微信集成开发完成记录.md
- docs/03-业务模块/IIT Manager Agent/04-开发计划/最小MVP闭环开发计划.md
- docs/03-业务模块/IIT Manager Agent/00-模块当前状态与开发指南.md
2026-01-03 09:39:39 +08:00
36ce1bbcb2 feat(iit): Complete Day 3 - WeChat Work integration and URL verification
Summary:
- Implement WechatService (314 lines, push notifications)
- Implement WechatCallbackController (501 lines, async reply mode)
- Complete iit_quality_check Worker with WeChat notifications
- Configure WeChat routes (GET + POST /wechat/callback)
- Configure natapp tunnel for local development
- WeChat URL verification test passed

Technical Highlights:
- Async reply mode to avoid 5-second timeout
- Message encryption/decryption using @wecom/crypto
- Signature verification using getSignature
- natapp tunnel: https://iit.nat100.top
- Environment variables configuration completed

Technical Challenges Solved:
- Fix environment variable naming (WECHAT_CORP_SECRET)
- Fix @wecom/crypto import (createRequire for CommonJS)
- Fix decrypt function parameters (2 params, not 4)
- Fix Token character recognition (lowercase l vs digit 1)
- Regenerate EncodingAESKey (43 chars, correct format)
- Configure natapp for internal network penetration

Test Results:
- WeChat developer tool verification: PASSED
- Return status: request success
- HTTP 200, decrypted 23 characters correctly
- Backend logs: URL verification successful

Documentation:
- Add Day3 WeChat integration development record
- Update MVP development task list (Day 2-3 completed)
- Update module status guide (v1.2 -> v1.3)
- Overall completion: 35% -> 50%

Progress:
- Module completion: 35% -> 50%
- Day 3 development: COMPLETED
- Ready for end-to-end testing (REDCap -> WeChat)
2026-01-03 00:13:36 +08:00
bdfca32305 docs(iit): REDCap对接技术方案完成与模块状态更新
- 新增《REDCap对接技术方案与实施指南》(1070行)
  - 确定DET+REST API技术方案(不使用External Module)
  - 完整RedcapAdapter/WebhookController/SyncManager代码设计
  - Day 2详细实施步骤与验收标准
- 更新《IIT Manager Agent模块当前状态与开发指南》
  - 记录REDCap本地环境部署完成(15.8.0)
  - 记录对接方案确定过程与技术决策
  - 更新Day 2工作计划(6个阶段详细清单)
  - 整体进度18%(Day 1完成+REDCap环境就绪)
- REDCap环境准备完成
  - 测试项目test0102(PID 16)创建成功
  - DET功能源码验证通过
  - 本地Docker环境稳定运行

技术方案:
- 实时触发: Data Entry Trigger (0秒延迟)
- 数据拉取: REST API exportRecords (增量同步)
- 轮询补充: pg-boss定时任务 (每30分钟)
- 可靠性: Webhook幂等性 + 轮询补充机制
2026-01-02 14:30:38 +08:00