CLQMS (Clinical Laboratory Quality Management System)

A REST API backend for modern clinical laboratory workflows.

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🤖 For Claude Code

When working in this repository, prioritize Serena MCP tools for code operations:

• Use find_symbol / get_symbols_overview instead of Read for exploring code structure
• Use replace_symbol_body instead of Edit for modifying functions, methods, classes
• Use insert_before_symbol / insert_after_symbol for adding new code symbols
• Use search_for_pattern instead of Grep for searching code patterns
• Use list_dir / find_file instead of Glob for file discovery

This minimizes tool calls and leverages semantic code understanding for this PHP codebase.

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CLQMS is a headless REST API backend designed to streamline laboratory operations, ensure data integrity, and manage complex diagnostic workflows. Built on a foundation of precision and regulatory compliance, this system provides comprehensive JSON endpoints for laboratory operations.

Key Characteristic: This is an API-only system with no view layer. Frontend applications (web, mobile, desktop) consume these REST endpoints to build laboratory information systems.

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🏛️ Core Architecture & Design

CLQMS is a headless REST API system following a clean architecture pattern. The system is designed to be consumed by any frontend client (web, mobile, desktop) through comprehensive JSON endpoints.

API-First Architecture:

• No View Layer: This system provides REST APIs only - no HTML views, no server-side rendering
• Frontend Agnostic: Any client can consume these APIs (React, Vue, Angular, mobile apps, desktop apps)
• JSON-First: All requests/responses use JSON format
• Stateless: Each API request is independent with JWT authentication

The system is currently undergoing a strategic Architectural Redesign to consolidate legacy structures into a high-performance, maintainable schema. This design focuses on reducing technical debt and improving data consistency across:

• Unified Test Definitions: Consolidating technical, calculated, and site-specific test data.
• Reference Range Centralization: A unified engine for numeric, threshold, text, and coded results.
• Ordered Workflow Management: Precise tracking of orders from collection to verification.

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🛡️ 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.

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🛠️ Technical Stack

Component	Specification
Language	PHP 8.1+ (PSR-compliant)
Framework	CodeIgniter 4 (API-only mode)
Security	JWT (JSON Web Tokens) Authorization
Database	MySQL (Optimized Schema Migration in progress)
API Format	RESTful JSON
Testing	PHPUnit 10.5+

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📂 Documentation & Specifications

Key Documents

Document	Location	Description
PRD	PRD.md	Complete Product Requirements Document (API-focused)
Technical Guide	CLAUDE.md	Architecture, coding standards, common commands
API Overview	This file	REST API documentation and endpoints
Database Migrations	app/Database/Migrations/	Database schema history

API Documentation

All API endpoints follow REST conventions:

Base URL: /api

Authentication: JWT token required for most endpoints (except /api/login, /api/demo/*)

Response Format:

{
  "status": "success|error",
  "message": "Human-readable message",
  "data": { ... }
}

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🔌 REST API Overview

API Endpoint Categories

Authentication & Authorization

Method	Endpoint	Description	Auth Required
POST	/api/login	User login, returns JWT token	No
POST	/api/logout	Invalidate JWT token	Yes
POST	/api/refresh	Refresh JWT token	Yes

Patient Management

Method	Endpoint	Description	Auth Required
GET	/api/patient	List patients with pagination	Yes
GET	/api/patient/{id}	Get patient details	Yes
POST	/api/patient	Create new patient	Yes
PATCH	/api/patient/{id}	Update patient	Yes
DELETE	/api/patient/{id}	Soft delete patient	Yes

Order Management

Method	Endpoint	Description	Auth Required
GET	/api/ordertest	List orders	Yes
GET	/api/ordertest/{id}	Get order details	Yes
POST	/api/ordertest	Create order	Yes
PATCH	/api/ordertest/{id}	Update order	Yes
DELETE	/api/ordertest/{id}	Delete order	Yes
POST	/api/ordertest/status	Update order status	Yes

Demo/Test Endpoints (No Auth)

Method	Endpoint	Description	Auth Required
POST	/api/demo/order	Create demo order with patient	No

Specimen Management

Method	Endpoint	Description	Auth Required
GET	/api/specimen	List specimens	Yes
GET	/api/specimen/{id}	Get specimen details	Yes
POST	/api/specimen	Create specimen	Yes
PATCH	/api/specimen/{id}	Update specimen	Yes
POST	/api/specimen/status	Update specimen status	Yes

Result Management

Method	Endpoint	Description	Auth Required
GET	/api/patresult	List patient results	Yes
GET	/api/patresult/{id}	Get result details	Yes
POST	/api/patresult	Enter new result	Yes
PATCH	/api/patresult/{id}	Update result	Yes
POST	/api/patresult/status	Verify result (VER/REV/REP)	Yes

Edge API (Instrument Integration)

Method	Endpoint	Description	Auth Required
POST	/api/edge/result	Receive instrument results	API Key
GET	/api/edge/order	Fetch pending orders	API Key
POST	/api/edge/order/{id}/ack	Acknowledge order	API Key
POST	/api/edge/status	Log instrument status	API Key

API Response Format

All API endpoints return JSON in this format:

Success Response:

{
  "status": "success",
  "message": "Operation completed successfully",
  "data": {
    // Response data here
  }
}

Error Response:

{
  "status": "error",
  "message": "Error description",
  "errors": [
    {
      "field": "field_name",
      "message": "Validation error message"
    }
  ]
}

Authentication

Most endpoints require JWT authentication:

Request Headers:

Authorization: Bearer {jwt_token}
Content-Type: application/json

Login Request Example:

POST /api/login
{
  "username": "labuser",
  "password": "password123"
}

Login Response:

{
  "status": "success",
  "message": "Login successful",
  "data": {
    "token": "eyJ0eXAiOiJKV1QiLCJhbGc...",
    "expires_in": 3600,
    "user": {
      "id": 1,
      "username": "labuser",
      "name": "Lab User"
    }
  }
}

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Lookups Library (app/Libraries/ValueSet.php)

CLQMS uses a JSON file-based lookup system loaded via App\Libraries\Lookups class. All lookup data is stored as JSON files in app/Libraries/Data/valuesets/ for easy maintenance and versioning.

How It Works

• Lookups class extends ValueSet which handles caching and file loading
• Each lookup is stored as app/Libraries/Data/valuesets/{name}.json
• Lookup names are lowercase with underscores (e.g., gender.json, order_priority.json)

Available Lookups

Lookup File	Description	Example Values
gender	Patient gender	Female, Male, Unknown
order_priority	Order priority levels	Stat, ASAP, Routine, Preop
order_status	Order lifecycle status	STC, SCtd, SArrv, SRcvd
specimen_type	Specimen types	BLD, SER, PLAS, UR, CSF
specimen_status	Specimen status	Ordered, Collected, Received
specimen_condition	Specimen quality flags	HEM, ITC, LIP, CLOT
specimen_activity	Specimen workflow events	COLLECT, RECEIVE, REJECT
result_type	Result data types	NMRIC, RANGE, TEXT, VSET
result_unit	Common measurement units	g/dL, mg/dL, x10^6/mL
result_status	Result validation status	Preliminary, Final, Corrected
test_type	Test definition types	TEST, PARAM, CALC, GROUP
test_activity	Test workflow activities	Order, Analyse, VER, REV
test_status	Test active status	Active, Inactive, Discontinued
priority	General priority values	STAT, HIGH, NORMAL, LOW
race	Ethnicity/race categories	Jawa, Sunda, Batak, etc.
religion	Religious affiliations	Islam, Kristen, Katolik, Hindu
marital_status	Marital status	Single, Married, Divorced
death_indicator	Death status flags	Yes, No
identifier_type	ID document types	KTP, Passport, SSN, SIM
operation	CRUD operation types	Create, Read, Update, Delete
site_type	Healthcare facility types	GH, PH, GHL, PHL, GL, PL
site_class	Facility classification	A, B, C, D, Utm, Ptm
ws_type	Workstation types	Primary, Secondary
enable_disable	Boolean toggle states	Enabled, Disabled
entity_type	Entity classification	Patient, Provider, Site
requested_entity	Requestor types	Physician, Nurse, Lab
location_type	Location categories	OPD, IPD, ER, LAB
area_class	Geographic classifications	Urban, Rural, Suburban
adt_event	ADT event types	Admission, Transfer, Discharge
body_site	Collection sites	Left Arm, Right Arm, Finger
collection_method	Specimen collection methods	Venipuncture, Fingerstick
container_size	Tube/container volumes	3mL, 5mL, 10mL
container_class	Container types	Vacutainer, Tube, Cup
container_cap_color	Tube cap colors	Red, Purple, Blue, Green
additive	Tube additives	EDTA, Heparin, Fluoride
fasting_status	Fasting requirement flags	Fasting, Non-Fasting
ethnic	Ethnicity categories	Various regional groups
math_sign	Mathematical operators	+, -, *, /, =, <, >
formula_language	Formula expression types	Formula, Expression
generate_by	Generation methods	Auto, Manual, Import
did_type	Device identification types	Serial, MAC, UUID
activity_result	Activity outcomes	Success, Fail, Retry
reference_type	Reference value types	NMRIC, TEXT, LIST
range_type	Range calculation types	REF, CRTC, VAL, RERUN
numeric_ref_type	Numeric ref types	Reference, Critical, Valid
text_ref_type	Text reference types	Normal, Abnormal, Critical
request_status	Request status	Pending, Approved, Rejected
v_category	ValueSet categories	Various categories

Usage

use App\Libraries\Lookups;

// Get all lookups (loads all JSON files, cached)
$allLookups = Lookups::getAll();

// Get single lookup formatted for dropdowns
$gender = Lookups::get('gender');
// Returns: [{"value":"1","label":"Female"},{"value":"2","label":"Male"},...]

// Get raw data without formatting
$raw = Lookups::getRaw('gender');
// Returns: [{"key":"1","value":"Female"},{"key":"2","value":"Male"},...]

// Get label for a specific key
$label = Lookups::getLabel('gender', '1'); // Returns 'Female'

// Get key/value pairs for select inputs
$options = Lookups::getOptions('gender');
// Returns: [["key":"1","value":"Female"],...]

// Transform database records with lookup text labels
$patients = [
    ['ID' => 1, 'Sex' => '1', 'Priority' => 'S'],
    ['ID' => 2, 'Sex' => '2', 'Priority' => 'R'],
];
$labeled = Lookups::transformLabels($patients, [
    'Sex' => 'gender',
    'Priority' => 'order_priority'
]);
// Result: [['ID'=>1, 'Sex'=>'1', 'SexText'=>'Female', 'Priority'=>'S', 'PriorityText'=>'Stat'],...]

// Clear cache after modifying valueset data
Lookups::clearCache();

When to Use

Approach	Use Case
Lookups Library	Server-side static values that rarely change (gender, status, types) - fast, cached
API /api/valueset*	Dynamic values managed by admins at runtime, or for frontend clients needing lookup data

Adding New Lookups

1. Create app/Libraries/Data/valuesets/{name}.json:

{
  "name": "example_lookup",
  "description": "Example lookup description",
  "values": [
    {"key": "1", "value": "Option One"},
    {"key": "2", "value": "Option Two"},
    {"key": "3", "value": "Option Three"}
  ]
}

2. Access via Lookups::get('example_lookup')

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📋 Master Data Management

CLQMS provides comprehensive master data management for laboratory operations. All master data is accessible via REST API endpoints.

🧪 Laboratory Tests

The Test Definitions module manages all laboratory test configurations including parameters, calculated tests, and test panels.

Test Types

Type Code	Description	Table
TEST	Individual laboratory test with technical specs	testdefsite + testdeftech
PARAM	Parameter value (non-lab measurement)	testdefsite + testdeftech
CALC	Calculated test with formula	testdefsite + testdefcal
GROUP	Panel/profile containing multiple tests	testdefsite + testdefgrp
TITLE	Section title for report organization	testdefsite

API Endpoints

Method	Endpoint	Description
GET	/api/tests	List all tests with optional filtering
GET	/api/tests/{id}	Get test details with type-specific data
POST	/api/tests	Create new test definition
PATCH	/api/tests	Update existing test
DELETE	/api/tests	Soft delete test (sets EndDate)

Filtering Parameters

• TestSiteName - Search by test name (partial match)
• TestType - Filter by test type VID (1-5)
• VisibleScr - Filter by screen visibility (0/1)
• VisibleRpt - Filter by report visibility (0/1)

Test Response Structure

{
  "status": "success",
  "message": "Data fetched successfully",
  "data": [
    {
      "TestSiteID": 1,
      "TestSiteCode": "CBC",
      "TestSiteName": "Complete Blood Count",
      "TestType": 4,
      "TypeCode": "GROUP",
      "TypeName": "Group Test",
      "SeqScr": 50,
      "VisibleScr": 1,
      "VisibleRpt": 1
    }
  ]
}

📏 Reference Ranges

Reference Ranges define normal and critical values for test results. The system supports multiple reference range types based on patient demographics.

Reference Range Types

Type	Table	Description
Numeric	refnum	Numeric ranges with age/sex criteria
Text	reftxt	Text-based reference values

Numeric Reference Range Structure

Field	Description
NumRefType	Type: REF (Reference), CRTC (Critical), VAL (Validation), RERUN
RangeType	RANGE or THOLD
Sex	Gender filter (0=All, 1=Female, 2=Male)
AgeStart	Minimum age (years)
AgeEnd	Maximum age (years)
LowSign	Low boundary sign (=, <, <=)
Low	Low boundary value
HighSign	High boundary sign (=, >, >=)
High	High boundary value
Flag	Result flag (H, L, A, etc.)

API Endpoints

Method	Endpoint	Description
GET	/api/refnum	List numeric reference ranges
GET	/api/refnum/{id}	Get reference range details
POST	/api/refnum	Create reference range
PATCH	/api/refnum	Update reference range
DELETE	/api/refnum	Soft delete reference range

📑 Value Sets

Value Sets are configurable dropdown options used throughout the system. Each Value Set Definition (VSetDef) contains multiple Value Set Values (ValueSet).

Value Set Hierarchy

valuesetdef (VSetDefID, VSName, VSDesc)
    └── valueset (VID, VSetID, VValue, VDesc, VOrder, VCategory)

Common Value Sets

VSetDefID	Name	Example Values
1	Priority	STAT (S), ASAP (A), Routine (R), Preop (P)
2	Enable/Disable	Disabled (0), Enabled (1)
3	Gender	Female (1), Male (2), Unknown (3)
10	Order Status	STC, SCtd, SArrv, SRcvd, SAna, etc.
15	Specimen Type	BLD, SER, PLAS, UR, CSF, etc.
16	Unit	L, mL, g/dL, mg/dL, etc.
27	Test Type	TEST, PARAM, CALC, GROUP, TITLE
28	Result Unit	g/dL, g/L, mg/dL, x10^6/mL, etc.
35	Test Activity	Order, Analyse, VER, REV, REP

API Endpoints

Method	Endpoint	Description
GET	/api/valuesetdef	List all value set definitions
GET	/api/valuesetdef/{id}	Get valueset with all values
GET	/api/valuesetdef/{id}/values	Get values for specific valueset
POST	/api/valuesetdef	Create new valueset definition
PATCH	/api/valuesetdef	Update valueset definition
DELETE	/api/valuesetdef	Delete valueset definition

Value Set Response Structure

{
  "status": "success",
  "data": {
    "VSetDefID": 27,
    "VSName": "Test Type",
    "VSDesc": "testdefsite.TestType",
    "values": [
      { "VID": 1, "VValue": "TEST", "VDesc": "Test", "VOrder": 1 },
      { "VID": 2, "VValue": "PARAM", "VDesc": "Parameter", "VOrder": 2 },
      { "VID": 3, "VValue": "CALC", "VDesc": "Calculated Test", "VOrder": 3 },
      { "VID": 4, "VValue": "GROUP", "VDesc": "Group Test", "VOrder": 4 },
      { "VID": 5, "VValue": "TITLE", "VDesc": "Title", "VOrder": 5 }
    ]
  }
}

📊 Database Tables Summary

Category	Tables	Purpose
Tests	testdefsite, testdeftech, testdefcal, testdefgrp, testmap	Test definitions
Reference Ranges	refnum, reftxt	Result validation
Value Sets	valuesetdef, valueset	Configurable options

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🔌 Edge API - Instrument Integration

The Edge API provides endpoints for integrating laboratory instruments via the tiny-edge middleware. Results from instruments are staged in the edgeres table before processing into the main patient results (patres).

Endpoints

Method	Endpoint	Description
POST	/api/edge/result	Receive instrument results (stored in edgeres)
GET	/api/edge/order	Fetch pending orders for an instrument
POST	/api/edge/order/:id/ack	Acknowledge order delivery to instrument
POST	/api/edge/status	Log instrument status updates

Workflow

Instrument → tiny-edge → POST /api/edge/result → edgeres table → [Manual/Auto Processing] → patres table

Key Features:

• Staging Table: All results land in edgeres first for validation
• Rerun Handling: Duplicate SampleID + TestSiteCode increments AspCnt in patres
• Configurable Processing: Auto or manual processing based on settings
• Status Tracking: Full audit trail via edgestatus and edgeack tables

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📜 Usage Notice

This is an API-only backend system. There are no views, HTML templates, or server-side rendering components. Frontend applications should consume these REST endpoints to build user interfaces for laboratory operations.

This repository contains proprietary information intended for the 5Panda Team and authorized collaborators.

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© 2025 5Panda Team. Engineering Precision in Clinical Diagnostics.