707f783229
feat(rvw): complete tenant portal polish and ops assignment fixes
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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
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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
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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
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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
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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
4a4771fbbe
fix(rvw): speed up review flow and complete forensics export
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Run RVW skills in controlled parallel mode and persist per-skill progress so users can view completed tabs during execution.
Also include data-forensics tables in Word export and refresh the RVW module status documentation.
Made-with: Cursor
2026-03-10 21:10:43 +08:00
097e7920ab
feat(admin): add user-level direct permission system and enhance activity tracking
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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
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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
5c5fec52c1
fix(aia,ssa,asl,infra): harden SSE transport and stabilize attachment context
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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
a666649fd4
feat(iit): harden QC pipeline consistency and release artifacts
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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
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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
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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
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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
aadceb5cde
feat(ssa): Implement dual-channel architecture Phase 1-3 (QPER + LLM Agent pipeline)
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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
2030ebe28f
feat(iit): Complete V3.1 QC engine + GCP business reports + AI timeline + bug fixes
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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
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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
9b8490b4d0
docs(iit): Update module status with frontend architecture changes
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Changes:
- Add frontend architecture adjustment milestone (admin/business side split)
- Document product positioning: ops team configures, end users use QC platform
- Add new completed feature section for routing/navigation changes
- Update current status to reflect Web AI Chat and admin IIT project management
Made-with: Cursor
2026-02-26 22:12:49 +08:00
205932bb3f
feat(asl): Complete Tool 4 SR Chart Generator and Tool 5 Meta Analysis Engine
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Tool 4 - SR Chart Generator:
- PRISMA 2020 flow diagram with Chinese/English toggle (SVG)
- Baseline characteristics table (Table 1)
- Dual data source: project pipeline API + Excel upload
- SVG/PNG export support
- Backend: ChartingService with Prisma aggregation
- Frontend: PrismaFlowDiagram, BaselineTable, DataSourceSelector
Tool 5 - Meta Analysis Engine:
- 3 data types: HR (metagen), dichotomous (metabin), continuous (metacont)
- Random and fixed effects models
- Multiple effect measures: HR / OR / RR
- Forest plot + funnel plot (base64 PNG from R)
- Heterogeneity statistics: I2, Q, p-value, Tau2
- Data input via Excel upload or project pipeline
- R Docker image updated with meta package (13 tools total)
- E2E test: 36/36 passed
- Key fix: exp() back-transformation for log-scale ratio measures
Also includes:
- IIT CRA Agent V3.0 routing and AI chat page integration
- Updated ASL module status guide (v2.3)
- Updated system status guide (v6.3)
- Updated R statistics engine guide (v1.4)
Tested: Frontend renders correctly, backend APIs functional, E2E tests passed
Made-with: Cursor
2026-02-26 21:51:02 +08:00
7c3cc12b2e
feat(iit): Complete CRA Agent V3.0 P1 - ChatOrchestrator with LLM Function Calling
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P1 Architecture: Lightweight ReAct (Function Calling loop, max 3 rounds)
Core changes:
- Add ToolDefinition/ToolCall types to LLM adapters (DeepSeek + CloseAI + Claude)
- Replace 6 old tools with 4 semantic tools: read_report, look_up_data, check_quality, search_knowledge
- Create ChatOrchestrator (~160 lines) replacing ChatService (1,442 lines)
- Wire WechatCallbackController to ChatOrchestrator, deprecate ChatService
- Fix nullable content (string | null) across 12+ LLM consumer files
E2E test results: 8/8 scenarios passed (100%)
- QC report query, critical issues, patient data, trend, on-demand QC
- Knowledge base search, project overview, data modification refusal
Net code reduction: ~1,100 lines
Tested: E2E P1 chat test 8/8 passed with DeepSeek API
Made-with: Cursor
2026-02-26 14:27:09 +08:00
31b0433195
docs(iit): Add CRA Agent V3.0 development plan and update module status guide
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V3.0 Plan:
- Finalize CRA Agent V3.0 development plan (replace CRA positioning)
- Add unified CRA QC platform PRD
- Add HTML UI prototype (dashboard, AI stream, eQuery, reports)
- Architecture: report-driven + LLM Tool Use + 4 semantic tools
Module Status Update:
- Update architecture from dual-brain V2.9.1 to V3.0 Tool Use
- Update DB schema inventory (5 tables -> 18 tables)
- Update code stats (577 lines -> 15,000+ lines / 61 files)
- Update next steps to V3.0 P0 roadmap
- Archive old phase plans (ReAct engine, IntentService)
- Add V3.0 document references (plan, PRD, prototype)
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-25 22:04:00 +08:00
f0736dbca1
feat(asl/extraction): Complete Tool 3 M1+M2 - skeleton pipeline and HITL workbench
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M1 Skeleton Pipeline:
- Scatter-dispatch + Aggregator polling pattern (PgBoss)
- PKB ACL bridge (PkbBridgeService -> PkbExportService DTOs)
- ExtractionSingleWorker with DeepSeek-V3 LLM extraction
- PermanentExtractionError for non-retryable failures
- Phantom Retry Guard (idempotent worker)
- 3-step minimal frontend (Setup -> Progress -> Workbench)
- 4 new DB tables (extraction_templates, project_templates, tasks, results)
- 3 system templates seed (RCT, Cohort, QC)
- M1 integration test suite
M2 HITL Workbench:
- MinerU VLM integration for high-fidelity table extraction
- XML-isolated DynamicPromptBuilder with flat JSON output template
- fuzzyQuoteMatch validator (3-tier confidence scoring)
- SSE real-time logging via ExtractionEventBus
- Schema-driven ExtractionDrawer (dynamic field rendering from template)
- Excel wide-table export with flattenModuleData normalization
- M2 integration test suite
Critical Fixes (data normalization):
- DynamicPromptBuilder: explicit flat key-value output format with example
- ExtractionExcelExporter: handle both array and flat data formats
- ExtractionDrawer: schema-driven rendering instead of hardcoded fields
- ExtractionValidator: array-format quote verification support
- SSE route: Fastify register encapsulation to bypass auth for EventSource
- LLM JSON sanitizer: strip illegal control chars before JSON.parse
Also includes: RVW stats verification spec, SSA expert config guide
Tested: M1 pipeline test + M2 HITL test + manual frontend verification
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-25 18:29:20 +08:00
371fa53956
docs(asl): Upgrade Tool 3 architecture from Fan-out to Scatter+Aggregator (v2.0)
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Architecture transformation:
- Replace Fan-out (Manager->Child->Last Child Wins) with Scatter+Aggregator pattern
- API layer directly dispatches N independent jobs (no Manager)
- Worker only writes its own Result row, never touches Task table (zero row-lock)
- Aggregator polls groupBy for completion + zombie cleanup (replaces Sweeper)
- Reduce red lines from 13 to 9, eliminate distributed complexity
Documents updated (10 files):
- 08-Tool3 main architecture doc: v2.0 rewrite (schema, Task 2.3/2.4, red lines, risks)
- 08d-Code patterns: rewrite sections 4.1-4.6 (API dispatch, SingleWorker, Aggregator)
- 08a-M1 sprint: rewrite M1-3 core (Worker+Aggregator), red lines, acceptance criteria
- 08b-M2 sprint: simplify SSE (NOTIFY/LISTEN downgraded to P2 optional)
- 08c-M3 sprint: milestone table wording update
- New: Scatter+Polling Aggregator pattern guide v1.1 (Level 2 cookbook)
- New: V2.0 architecture deep review and gap-fix report
- Updated: ASL module status, system status, capability layer index
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-24 22:11:09 +08:00
85fda830c2
feat(ssa): Complete Phase V-A editable analysis plan variables
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Features:
- Add editable variable selection in workflow plan (SingleVarSelect + MultiVarTags)
- Implement 3-layer flexible interception (warning bar + icon + blocking dialog)
- Add tool_param_constraints.json for 12 statistical tools parameter validation
- Add PATCH /workflow/:id/params API with Zod structural validation
- Implement synchronous parameter sync before execution (Promise chaining)
- Fix LLM hallucination by strict system prompt constraints
- Fix DynamicReport object-based rows compatibility (R baseline_table)
- Fix Word export row.map error with same normalization logic
- Restore inferGroupingVar for smart default variable selection
- Add ReactMarkdown rendering in SSAChatPane
- Update SSA module status document to v3.5
Modified files:
- backend: workflow.routes, ChatHandlerService, SystemPromptService, FlowTemplateService
- frontend: WorkflowTimeline, SSAWorkspacePane, DynamicReport, SSAChatPane, ssaStore, ssa.css
- config: tool_param_constraints.json (new)
- docs: SSA status doc, team review reports
Tested: Cohort study end-to-end execution + report export verified
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-24 13:08:29 +08:00
dc6b292308
docs(asl): Complete Tool 3 extraction workbench V2.0 development plan (v1.5)
...
ASL Tool 3 Development Plan:
- Architecture blueprint v1.5 (6 rounds of architecture review, 13 red lines)
- M1/M2/M3 sprint checklists (Skeleton Pipeline / HITL Workbench / Dynamic Template Engine)
- Code patterns cookbook (9 chapters: Fan-out, Prompt engineering, ACL, SSE dual-track, etc.)
- Key patterns: Fan-out with Last Child Wins, Optimistic Locking, teamConcurrency throttling
- PKB ACL integration (anti-corruption layer), MinerU Cache-Aside, NOTIFY/LISTEN cross-pod SSE
- Data consistency snapshot for long-running extraction tasks
Platform capability:
- Add distributed Fan-out task pattern development guide (7 patterns + 10 anti-patterns)
- Add system-level async architecture risk analysis blueprint
- Add PDF table extraction engine design and usage guide (MinerU integration)
- Add table extraction source code (TableExtractionManager + MinerU engine)
Documentation updates:
- Update ASL module status with Tool 3 V2.0 plan readiness
- Update system status document (v6.2) with latest milestones
- Add V2.0 product requirements, prototypes, and data dictionary specs
- Add architecture review documents (4 rounds of review feedback)
- Add test PDF files for extraction validation
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-23 22:49:16 +08:00
8f06d4f929
feat(asl): Complete Deep Research V2.0 core development
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Backend:
- Add SSE streaming client (unifuncsSseClient) replacing async polling
- Add paragraph-based reasoning parser with mergeConsecutiveThinking
- Add requirement expansion service (DeepSeek-V3 PICOS+MeSH)
- Add Word export service with Pandoc, inline hyperlinks, reference link expansion
- Add deep research V2 worker with 2s log flush and Chinese source prompt
- Add 5 curated data sources config (PubMed/ClinicalTrials/Cochrane/CNKI/MedJournals)
- Add 4 API endpoints (generate-requirement/tasks/task-status/export-word)
- Update Prisma schema with 6 new V2.0 fields on AslResearchTask
- Add DB migration for V2.0 fields
- Simplify ASL_DEEP_RESEARCH_EXPANSION prompt (remove strategy section)
Frontend:
- Add waterfall-flow DeepResearchPage (phase 0-4 progressive reveal)
- Add LandingView, SetupPanel, StrategyConfirm, AgentTerminal, ResultsView
- Add react-markdown + remark-gfm for report rendering
- Add custom link component showing visible URLs after references
- Add useDeepResearchTask polling hook
- Add deep research TypeScript types
Tests:
- Add E2E test, smoke test, and Chinese data source test scripts
Docs:
- Update ASL module status (v2.0 - core features complete)
- Update system status (v6.1 - ASL V2.0 milestone)
- Update Unifuncs DeepSearch API guide (v2.0 - SSE mode + Chinese source results)
- Update module auth specification (test script guidelines)
- Update V2.0 development plan
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-23 13:21:52 +08:00
b06daecacd
feat(asl): Add Deep Research V2.0 development plan and Unifuncs API site coverage testing
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Completed:
- Unifuncs DeepSearch API site coverage test (18 medical sites, 9 tier-1 available)
- ClinicalTrials.gov dedicated test (4 strategies, English query + depth>=10 works best)
- Deep Research V2.0 development plan (5-day phased delivery)
- DeepResearch engine capability guide (docs/02-common-capability/)
- Test scripts: test-unifuncs-site-coverage.ts, test-unifuncs-clinicaltrials.ts
Key findings:
- Tier-1 sites: PubMed(28), ClinicalTrials(38), NCBI(18), Scholar(10), Cochrane(4), CNKI(7), SinoMed(9), GeenMedical(5), VIP(1)
- Paid databases (WoS/Embase/Scopus/Ovid) cannot be accessed (no credential support)
- ClinicalTrials.gov requires English queries with max_depth>=10
Updated: ASL module status doc, system status doc, common capability list
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-22 22:44:41 +08:00
3446909ff7
feat(ssa): Complete Phase I-IV intelligent dialogue and tool system development
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Phase I - Session Blackboard + READ Layer:
- SessionBlackboardService with Postgres-Only cache
- DataProfileService for data overview generation
- PicoInferenceService for LLM-driven PICO extraction
- Frontend DataContextCard and VariableDictionaryPanel
- E2E tests: 31/31 passed
Phase II - Conversation Layer LLM + Intent Router:
- ConversationService with SSE streaming
- IntentRouterService (rule-first + LLM fallback, 6 intents)
- SystemPromptService with 6-segment dynamic assembly
- TokenTruncationService for context management
- ChatHandlerService as unified chat entry
- Frontend SSAChatPane and useSSAChat hook
- E2E tests: 38/38 passed
Phase III - Method Consultation + AskUser Standardization:
- ToolRegistryService with Repository Pattern
- MethodConsultService with DecisionTable + LLM enhancement
- AskUserService with global interrupt handling
- Frontend AskUserCard component
- E2E tests: 13/13 passed
Phase IV - Dialogue-Driven Analysis + QPER Integration:
- ToolOrchestratorService (plan/execute/report)
- analysis_plan SSE event for WorkflowPlan transmission
- Dual-channel confirmation (ask_user card + workspace button)
- PICO as optional hint for LLM parsing
- E2E tests: 25/25 passed
R Statistics Service:
- 5 new R tools: anova_one, baseline_table, fisher, linear_reg, wilcoxon
- Enhanced guardrails and block helpers
- Comprehensive test suite (run_all_tools_test.js)
Documentation:
- Updated system status document (v5.9)
- Updated SSA module status and development plan (v1.8)
Total E2E: 107/107 passed (Phase I: 31, Phase II: 38, Phase III: 13, Phase IV: 25)
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-22 18:53:39 +08:00
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
11676f2840
fix(ssa): Fix 7 integration bugs and refactor frontend unified state management
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Bug fixes:
- Fix garbled error messages in chat (TypeWriter rendering issue)
- Fix R engine NA crash in descriptive.R (defensive isTRUE/is.na checks)
- Fix intent misclassification for statistical significance queries
- Fix step 2 results not displayed (accept warning status alongside success)
- Fix incomplete R code download (only step 1 included)
- Fix multi-task state confusion (clicking old card shows new results)
- Add R engine and backend parameter logging for debugging
Refactor - Unified Record Architecture:
- Replace 12 global singleton fields with AnalysisRecord as single source of truth
- Remove isWorkflowMode branching across all components
- One Analysis = One Record = N Steps paradigm
- selectRecord only sets currentRecordId, all rendering derives from currentRecord
- Fix cross-hook-instance issue: executeWorkflow fallback to store currentRecordId
Updated files: ssaStore, useWorkflow, useAnalysis, SSAChatPane, SSAWorkspacePane,
SSACodeModal, WorkflowTimeline, QueryService, WorkflowExecutorService, descriptive.R
Tested: Manual integration test passed - multi-task switching, R code completeness
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-21 22:58:59 +08:00
371e1c069c
feat(ssa): Complete QPER architecture - Query, Planner, Execute, Reflection layers
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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
428a22adf2
feat(ssa): Complete Phase 2A frontend integration - multi-step workflow end-to-end
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Phase 2A: WorkflowPlannerService, WorkflowExecutorService, Python data quality, 6 bug fixes, DescriptiveResultView, multi-step R code/Word export, MVP UI reuse. V11 UI: Gemini-style, multi-task, single-page scroll, Word export. Architecture: Block-based rendering consensus (4 block types). New R tools: chi_square, correlation, descriptive, logistic_binary, mann_whitney, t_test_paired. Docs: dev summary, block-based plan, status updates, task list v2.0.
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-20 23:09:27 +08:00
23b422f758
docs(ssa): Add SSA-Pro vision design - ideal intelligent statistical analysis system with 5 core capabilities
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Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-20 15:10:12 +08:00
a792b2e4be
docs(ssa): Update task list - Phase 1 progress 96%, add V11 UI tasks and daily standup 2026-02-20
...
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-20 14:51:06 +08:00
8d496d1515
feat(ssa): Complete V11 UI development and frontend-backend integration - Pixel-perfect V11 UI, multi-task support, Word export, input overlay fix, code cleanup. MVP Phase 1 core 95% complete.
...
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-20 14:46:45 +08:00
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
8137e3cde2
feat(ssa): Complete SSA-Pro MVP development plan v1.3
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Summary:
- Add PRD and architecture design V4 (Brain-Hand model)
- Complete 5 development guide documents
- Pass 3 rounds of team review (v1.0 -> v1.3)
- Add module status guide document
- Update system status document
Key Features:
- Brain-Hand architecture: Node.js + R Docker
- Statistical guardrails with auto degradation
- HITL workflow: PlanCard -> ExecutionTrace -> ResultCard
- Mixed data protocol: inline vs OSS
- Reproducible R code delivery
MVP Scope: 10 statistical tools
Status: Design 100%, ready for development
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-18 21:58:37 +08:00
f9ed0c2528
feat(rvw): Complete V2.0 Week 3 - Statistical validation extension and UX improvements
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Week 3 Development Summary:
- Implement negative sign normalization (6 Unicode variants)
- Enhance T-test validation with smart sample size extraction
- Enhance SE triangle and CI-P consistency validation with subrow support
- Add precise sub-cell highlighting for P-values in multi-line cells
- Add frontend issue type Chinese translations (6 new types)
- Add file format tips for PDF/DOC uploads
Technical improvements:
- Add _clean_statistical_text() in extractor.py
- Add _safe_float() wrapper in validator.py
- Add ForensicsReport.tsx component
- Update ISSUE_TYPE_LABELS translations
Documentation:
- Add 2026-02-18 development record
- Update RVW module status (v5.1)
- Update system status (v5.2)
Status: Week 3 complete, ready for Week 4 testing
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-18 18:26:16 +08:00
9f256c4a02
feat(rvw): implement Skills architecture (Day 7-10)
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- Add Skills core framework (types, registry, executor, profile, context)
- Implement DataForensicsSkill with DI, path security, graceful degradation
- Implement EditorialSkill and MethodologySkill wrapping existing services
- Extend ExtractionClient with IExtractionClient interface and analyzeDocx
- Refactor reviewWorker to support V1/V2 architecture switching
- Add Zod config validation and generic type support
- Update development docs and module status
Day 7: Skills core framework (~700 lines)
Day 8: DataForensicsSkill + ExtractionClient extension (~400 lines)
Day 9: EditorialSkill + MethodologySkill (~350 lines)
Day 10: ReviewWorker integration (~280 lines)
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-18 10:09:40 +08:00
e785969e54
feat(rvw): Implement RVW V2.0 Data Forensics Module - Day 6 StatValidator
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Summary:
- Implement L2 Statistical Validator (CI-P consistency, T-test reverse)
- Implement L2.5 Consistency Forensics (SE Triangle, SD>Mean check)
- Add error/warning severity classification with tolerance thresholds
- Support 5+ CI formats parsing (parentheses, brackets, 95% CI prefix)
- Complete Python forensics service (types, config, validator, extractor)
V2.0 Development Progress (Week 2 Day 6):
- Day 1-5: Python service setup, Word table extraction, L1 arithmetic validator
- Day 6: L2 StatValidator + L2.5 consistency forensics (promoted from V2.1)
Test Results:
- Unit tests: 4/4 passed (CI-P, SE Triangle, SD>Mean, T-test)
- Real document tests: 5/5 successful, 2 reasonable WARNINGs
Status: Day 6 completed, ready for Day 7 (Skills Framework)
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-17 22:15:27 +08:00
7a299e8562
feat(iit): Implement event-level QC architecture V3.1 with dynamic rule filtering, report deduplication and AI intent enhancement
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Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-08 21:22:11 +08:00
45c7b32dbb
docs(iit): Add QC system UI and LLM format optimization plan
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- 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
5db4a7064c
feat(iit): Implement real-time quality control system
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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
0c590854b5
docs(iit): Add IIT Manager Agent V2.9 development plan with multi-agent architecture
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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
4b9b90ffb8
feat(iit): Complete REDCap production deployment on Alibaba Cloud ECS
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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
aaa29ea9d3
feat(admin): Implement Prompt knowledge base integration
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Features:
- PromptService enhancement: enhanceWithKnowledge(), loadFullKnowledge(), ragSearch()
- FULL mode: Load entire knowledge base content
- RAG mode: Vector search based on user query
- Knowledge config API: PUT /:code/knowledge-config
- Test render with knowledge injection support
- Frontend: Knowledge config UI in Prompt editor
Bug fixes:
- Fix knowledge config not returned in getPromptDetail
- Fix publish button 400 error (empty request body)
- Fix cache not invalidated after publish
- Add detailed logging for debugging
Documentation:
- Add development record 2026-01-28
- Update ADMIN module status to Phase 4.6
- Update system status document to v4.5
Co-authored-by: Cursor <cursoragent@cursor.com >
2026-02-01 20:26:20 +08:00
0d9e6b9922
feat(admin): Implement System Knowledge Base management module
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Features:
- Backend: SystemKbService with full CRUD (knowledge bases + documents)
- Backend: 8 RESTful API endpoints (list/detail/create/update/delete/upload/download)
- Backend: OSS storage integration (system/knowledge-bases/{kbId}/{docId})
- Backend: RAG engine integration (document parsing, chunking, vectorization)
- Frontend: SystemKbListPage with card-based layout
- Frontend: SystemKbDetailPage with document management table
- Frontend: Master-Detail UX pattern for better user experience
- Document upload (single/batch), download (preserving original filename), delete
Technical:
- Database migration for system_knowledge_bases and system_kb_documents tables
- OSSAdapter.getSignedUrl with Content-Disposition for original filename
- Reuse RAG engine from common/rag for document processing
Tested: Local environment verified, all features working
2026-01-28 21:57:44 +08:00
3a4aa9123c
feat: Add Personal Center module and UI improvements
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- Add ProfilePage with avatar upload, password change, and module status display
- Update logo and favicon for login page and browser tab
- Redirect Data Cleaning module default route to Tool C
- Hide Settings button from top navigation for MVP
- Add avatar display in top navigation bar with refresh sync
- Add Prompt knowledge base integration development plan docs
2026-01-28 18:18:09 +08:00
bbf98c4d5c
fix(backend): Resolve PgBoss infinite loop issue and cleanup unused files
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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
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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
