lx-annotate Documentation

Welcome to the developer and maintainer documentation for lx-annotate. These pages cover data modeling conventions, implementation details, and automation workflows used throughout the project.

Contents

Guides

• General Documentation Guide
  • Who This Is For
  • Documentation Structure
  • Recommended Reading Paths
  • Quick Start
  • Support Notes
• Deployment Strategy
  • Overview
  • Preferred Production Path
  • Build Strategy
  • Runtime Strategy
  • Storage Recommendations
  • Service Topology
  • Ingress Contract
  • Hub Export Contract
  • Current Service Environment
  • LuxNix Audit Findings
  • Data Recovery Unit
  • Reverse Proxy Strategy
  • LuxNix Strategy
  • Current Limits
  • Related Guides
• Encrypted Storage Process
  • Scope
  • Summary
  • Key Loading
  • On-Disk Format
  • Write Path
  • Read Path
  • Random Access And Indexing
  • How Encryption Is Detected
  • Repair Path For Accidentally Plaintext Files
  • Verification Command
  • Operational Notes
  • Related Files
• Hub Export Workflow
  • Scope
  • Core Decisions
  • Marked For Upload
  • Eligible Resources
  • Sender State Machine
  • Transfer Identity
  • Transfer Mode Policy
  • Retry And Reuse Rules
  • Sender Payload Responsibilities
  • UI Workflow
  • Operational Requirements
  • Audit Requirements
  • Local Cleanup Policy
  • Summary
• Frontend Asset Deployment Contract
  • Contract Summary
  • Deployment Flow
  • Why emptyOutDir Is Disabled
  • Smoke Tests
  • Frame Annotation Integration Note
• Wheel Deployment
  • Scope
  • Host Packages
  • Runtime Contract
  • Ingress Contract
  • Storage Recommendations
  • Hub Deployment Profile
  • Secure Hub Transfer
  • Deployment
  • Current Services
  • LuxNix Permission Contract
  • Data Recovery Behavior
  • Failure Recovery
  • Service Isolation
  • Auth Caveat
  • Nginx Handoff
  • Notes
• Reporting Template & Requirement Sets Page (TemplateRequirementsPage)
  • Audience and Purpose
  • Where This Page Is Used
  • What You See on the Page
  • Why Requirement Sets Matter (Clinical View)
  • Typical Step-by-Step Workflow
  • Full Reporting Flow (All Steps)
  • Related Specialized Guides
  • Quick Practical Path for Clinical Documentation
  • Deep Link Behavior
  • Field and Button Reference
  • Developer Mapping: Requirement Objects to lx_dtypes Validators
  • Common Problems and Practical Fixes
  • Training Checklist (For Clinical Onboarding)
  • Glossary (Plain Language)
  • Related Technical Files (for Admins/Developers)
• AI Training Data Export
  • Data Safety Boundary
  • Recommended User Workflow
  • Export Output
  • API Example
  • Management Command Example
  • Standardized AI Dataset JSON
  • GastroNet-Style Training
  • Practical Checks
• Segment Annotation Workflow
  • Target Audience
  • Primary Component
  • Clinical Purpose
  • How Users Enter This Workflow
  • Preconditions
  • Step-by-Step for Medical Users
  • What Happens on Full Validation
  • Training Notes
  • Common Issues
  • Technical References
• Anonymization Validation and Correction Workflow
  • Target Audience
  • Primary Components
  • Clinical Purpose
  • Validation Workflow
  • Correction Workflow
  • Operational Recommendations
  • Common Issues
  • Technical References
• Dates and Times
  • 1. Always Use Strong Typing
  • 2. Enforce Timezone Awareness
  • 3. Stick to ISO 8601 Standards
  • 4. Validate Business Logic
  • 5. Handle “Now” and Defaults
  • 6. Serialization
  • Summary Checklist
  • 7. Complete Example
• Pydantic V2 Cheat Sheet
  • The Pydantic V2 Lifecycle
  • 1. Shared Base Model
  • 2. DateTime & Timezones (Strict Mode)
  • 3. Reusable Fields (Mixins)
  • 4. Advanced Validation Patterns
  • 5. Computed Fields (Derived Data)
  • 6. Managing Aliases (Frontend vs Backend)
  • 7. Path Objects & Filesystems
  • 8. YAML Fixtures & Sample Data
  • Summary Table: Validator Modes
• Dtypes Findings Migration (Incremental, Endoreg-Safe)
  • Scope
  • Current-State Inventory
  • Phased Checklist
  • Compatibility Matrix
  • Decision Log
  • Progress Log
  • Cutover Gate
• Core Concept Contract
  • Purpose
  • Core Concepts
  • Source-Of-Truth Order
  • Identity Rule
  • Collection Rule
  • API Surface
  • Drift Audit
• Core Concept Readiness Verdict
  • Purpose
  • Current Foundation (Implemented)
  • Verdict by Core Concept
  • Open Conceptual Decisions (Blocking Full Semantic Automation)
  • Opinion on report_templates.yaml
  • Governance Recommendation
  • Source-Of-Truth Order (Canonical)
• Core Concept Type Matrix
  • Classification
  • ClassificationChoice
  • ClassificationChoiceDescriptor
  • Examination
  • Finding
  • FindingType
  • Indication
  • IndicationType
  • Intervention
  • InterventionType
  • Unit
  • UnitType
  • InformationSource
  • InformationSourceType
  • Citation
• Reporting Template & Requirement Sets Page (TemplateRequirementsPage)
  • Audience and Purpose
  • Where This Page Is Used
  • What You See on the Page
  • Why Requirement Sets Matter (Clinical View)
  • Typical Step-by-Step Workflow
  • Full Reporting Flow (All Steps)
  • Quick Practical Path for Clinical Documentation
  • Deep Link Behavior
  • Field and Button Reference
  • Developer Mapping: Requirement Objects to lx_dtypes Validators
  • Common Problems and Practical Fixes
  • Training Checklist (For Clinical Onboarding)
  • Glossary (Plain Language)
  • Related Technical Files (for Admins/Developers)

API Reference

• API Reference

Quick Links

• Project repository: https://github.com/wg-lux/lx-annotate

• Issue tracker: https://github.com/wg-lux/lx-annotate/issues