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clqms-be/.serena/memories/project_overview.md
mahdahar 282c642da6 feat: add OpenSpec workflow, Serena integration, User API, and Specimen delete endpoint 
- Add OpenSpec experimental workflow with commands (opsx-apply, opsx-archive, opsx-explore, opsx-propose)
- Add Serena memory system for project context
- Implement User API (UserController, UserModel, routes)
- Add Specimen delete endpoint
- Update Test definitions and Routes
- Sync API documentation (OpenAPI)
- Archive completed 2026-03-08-backend-specs change
2026-03-09 07:00:12 +07:00

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CLQMS Project Overview

Project Purpose

CLQMS (Clinical Laboratory Quality Management System) is a headless REST API backend designed for modern clinical laboratory workflows. This API-only system provides comprehensive JSON endpoints for laboratory operations without any view layer. Frontend applications (web, mobile, desktop) consume these REST endpoints to build laboratory information systems.

Core Features

  • Patient registration and management
  • Laboratory test ordering and tracking
  • Specimen lifecycle management (collection → transport → reception → prep → analysis)
  • Result entry with reference range validation
  • Multi-level result verification (Technical → Clinical → Reporting)
  • Instrument integration via Edge API (tiny-edge middleware)
  • Master data management (value sets, test definitions, reference ranges)
  • Quality control and calibration tracking

Product Vision

To provide a headless, API-first laboratory information system serving as the backend for any frontend client while streamlining laboratory operations, ensuring regulatory compliance, and integrating seamlessly with laboratory instruments.

Technology Stack

Component Specification
Language PHP 8.1+ (PSR-compliant)
Framework CodeIgniter 4 (API-only mode)
Database MySQL 8.0+
Security JWT (JSON Web Tokens) via firebase/php-jwt
Testing PHPUnit 10.5+
API Format RESTful JSON
Architecture Clean architecture, API-first design

Key Dependencies

  • codeigniter4/framework - Main framework
  • firebase/php-jwt - JWT authentication
  • fakerphp/faker - Test data generation
  • phpunit/phpunit - Unit/feature testing

Strategic Pillars

  • Precision & Accuracy: Strict validation for all laboratory parameters and reference ranges
  • Scalability: Optimized for high-volume diagnostic environments
  • Compliance: Built-in audit trails and status history for full traceability
  • Interoperability: Modular architecture designed for LIS, HIS, and analyzer integrations

Key Characteristics

  • API-Only: No view layer, no server-side rendering
  • Frontend Agnostic: Any client can consume these APIs
  • JSON-First: All requests/responses use JSON format
  • Stateless: Each API request is independent with JWT authentication
  • UTC Normalization: Automatic UTC timestamp handling via BaseModel

Current Architecture Status

The system is undergoing an Architectural Redesign to consolidate legacy structures into a high-performance, maintainable schema focusing on:

  • Unified Test Definitions (consolidating technical, calculated, and site-specific test data)
  • Reference Range Centralization (unified engine for numeric, threshold, text, and coded results)
  • Ordered Workflow Management (precise tracking of orders from collection to verification)