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Version: 3.0.1

SDD Master Index

Date: 2026-01-18 Purpose: Central navigation for all SDD documentation

Document Overview​

DocumentPurposeStatusLine Count
sdd-architecture.mdSystem structure, AWS components & design patterns98%1251
sdd-algorithms.mdLogic, workflows, rules engine & data processing100%1944
sdd-configuration.mdEnvironment variables & kit settings100%869
sdd-deployment-operations.mdVapor, Cognito & environment setup90%195
sdd-security.mdAuthentication, authorization & AI security100%446
std-ui-testability.mdHTML attributes for automated testing (migrated to STD)100%101
sdd-testing.mdBehat testing infrastructure100%316
sdd-references.mdIEEE template, coding standards, UI refs70%422

Quick Navigation by Topic​

Authentication & Security​

TopicPrimary DocSectionRelated Docs
Cognito Authenticationsdd-security.mdAuthentication and Authorisationsdd-architecture.md, sdd-deployment-operations.md
Cognito User Pool Setupsdd-deployment-operations.mdCognito User Pool Setupsdd-security.md
JWT Token Handlingsdd-security.mdAuthentication Token Architecturesdd-algorithms.md (API Authentication)
SAML/SSO Integrationsdd-security.mdArchitecture (Flowchart)sdd-deployment-operations.md
AWS Programmatic Access Keyssdd-security.mdAWS Programmatic Access Key Privileges-
MFA Configurationsdd-security.mdRelated SRS Requirementssdd-configuration.md
Role-Based Access Controlsdd-security.mdRelated SRS Requirements-
AI Prompt Injection Preventionsdd-security.mdAI Prompt Injection Prevention-
Rate Limitingsdd-security.mdAI Prompt Injection Preventionsdd-algorithms.md
Authentication Middlewaresdd-security.mdAuthentication Middleware-
Security Headerssdd-security.mdSecurity Headers-

Data Processing & Analysis​

TopicPrimary DocSectionRelated Docs
Run Import Processsdd-algorithms.mdRun Import Processsdd-architecture.md (S3)
Run Analysissdd-algorithms.mdRun Analysissdd-algorithms.md (Rules Engine)
Parser API Integrationsdd-algorithms.mdParse Run Filesdd-configuration.md (Vapor Secrets)
DXAI Calibratorsdd-algorithms.mdAnalyse Run Filesdd-configuration.md
JSON Schema (Run Data)sdd-algorithms.mdConvert to standard JSON format-
File Validationsdd-algorithms.mdValidate Run file-
Storage Workflowsdd-algorithms.mdStore Run Filesdd-architecture.md (S3, Aurora)
Curve Alignment Algorithmsdd-algorithms.mdCurve Alignment Algorithm-
Trends Report Data Cachingsdd-algorithms.mdTrends Report Data Cachingsdd-configuration.md
Daily Outcomes Tablesdd-algorithms.mdDaily Outcomes Materialized Cache-
Feature Import/Cascadesdd-algorithms.mdFeature Import/Cascade Systemsdd-configuration.md
Role Alias to Rolesdd-algorithms.mdRole Alias to Role Workflow-
Real-Time Event Broadcastingsdd-algorithms.mdReal-Time Event Broadcastingsdd-architecture.md
Asynchronous Job Processingsdd-algorithms.mdAsynchronous Job Processingsdd-architecture.md

Rules Engine​

TopicPrimary DocSectionRelated Docs
Rules Introductionsdd-algorithms.mdRules Introductionsdd-configuration.md (Rules Mapping)
Rule Execution Flowsdd-algorithms.mdRunning Rules Architecture-
Rule Mapping Architecturesdd-algorithms.mdUnderstanding How Codes Worksdd-configuration.md
Westgard 1:2S Rulesdd-algorithms.md1:2S rulesdd-configuration.md (Westgard Limits)
Westgard 1:3S Rulesdd-algorithms.md1:3S rulesdd-configuration.md (Westgard Limits)
Westgard 2:2S Rulesdd-algorithms.md2:2S rulesdd-configuration.md (Westgard Limits)
Westgard 7T Rulesdd-algorithms.md7T rulesdd-configuration.md (Westgard Limits)
Combined Outcomessdd-algorithms.mdCombined Outcomes Algorithmsdd-configuration.md (Combined Outcomes)

Configuration​

TopicPrimary DocSectionRelated Docs
Vapor Environment Variablessdd-configuration.mdVapor Environment Variablessdd-deployment-operations.md
Vapor Secretssdd-configuration.mdVapor Secretssdd-deployment-operations.md
Client Configurationsdd-configuration.mdClient Configuration-
Control Labelssdd-configuration.mdControl Labels Configurationssdd-algorithms.md (Role matching)
Combined Outcomes Configsdd-configuration.mdCombined Outcomes Excel schemasdd-algorithms.md
Alerts Configurationsdd-configuration.mdAlerts Configurations-
Cross Contamination Limitssdd-configuration.mdCross Contamination Limits-
Curve Control Limitssdd-configuration.mdCurve Control Limits-
Delta CT Configurationsdd-configuration.mdDelta CT Configurations-
Error Codessdd-configuration.mdError Codes Configurations-
Error Resolutionssdd-configuration.mdError Resolutions Configurations-
Extractionssdd-configuration.mdExtractions Configurations-
Features (Toggles)sdd-configuration.mdFeatures Configurations-
Help Itemssdd-configuration.mdHelp Items Configurations-
Known Quantitiessdd-configuration.mdKnown Quantities Configurations-
LIMS Exportssdd-configuration.mdLims Exports Configurations-
Mix and Targetssdd-configuration.mdMix and Targets Configurationssdd-algorithms.md
QIR Settingssdd-configuration.mdQIR - Quantification Settings-
Qualitative Reportingsdd-configuration.mdQualitative Reportings Configurations-
Rules Mappingsdd-configuration.mdRules Mapping Configurationssdd-algorithms.md
Test Codessdd-configuration.mdTest Codes Configurations-
Thermocyclerssdd-configuration.mdThermocyclers Configurationssdd-algorithms.md
Westgard Limitssdd-configuration.mdWestgard Limits Configurationssdd-algorithms.md (Westgard Rules)
Dyessdd-configuration.mdDyes Configurations-
Rolessdd-configuration.mdRoles Configurations-
Rules Settingssdd-configuration.mdRules Configurationssdd-algorithms.md
Westgard Eventssdd-configuration.mdWestgard Events Configurationssdd-algorithms.md
Specimenssdd-configuration.mdSpecimens Configurations-

AWS Infrastructure​

TopicPrimary DocSectionRelated Docs
AWS Lambdasdd-architecture.mdAWS Lambdasdd-algorithms.md (Dependencies)
Amazon Cognitosdd-architecture.mdAmazon Cognitosdd-security.md, sdd-deployment-operations.md
Amazon ElastiCachesdd-architecture.mdAmazon ElastiCache-
Amazon RDS/Aurorasdd-architecture.mdAmazon RDS with Amazon Aurora Serverless v2sdd-algorithms.md
Amazon S3sdd-architecture.mdAmazon S3sdd-algorithms.md (Storage)
Amazon SQSsdd-architecture.mdAmazon Simple Queue Servicesdd-algorithms.md
Amazon SESsdd-architecture.mdAmazon Simple Email Service-
Amazon DynamoDBsdd-architecture.mdAmazon DynamoDB-
Pusher (Real-time)sdd-architecture.mdPushersdd-algorithms.md
System Workflow Diagramsdd-architecture.mdWorkflow using PCR.AI System-
Database Migrationsdd-architecture.mdServer Database Type Migration-

Deployment & Operations​

TopicPrimary DocSectionRelated Docs
Vapor Secret Configurationsdd-deployment-operations.mdVapor Secret in Deployment Consolesdd-configuration.md
Cognito User Pool Setupsdd-deployment-operations.mdProcess for setting up new Cognito user poolssdd-security.md
Environment URL Changessdd-deployment-operations.mdChanging environment subdomain URL-
Cloudflare DNSsdd-deployment-operations.mdChange domain CNAME in cloudflare-
Laravel Environment Variablessdd-deployment-operations.mdUpdate Laravel Environment Variablessdd-configuration.md

Configuration Import/Export​

TopicPrimary DocSectionRelated Docs
Configuration Uploadsdd-algorithms.mdConfiguration Upload Algorithmsdd-configuration.md
Configuration Exportsdd-algorithms.mdConfiguration Export Algorithmsdd-configuration.md
Excel Schema (Control Labels)sdd-configuration.mdControl Labels Excel Configurations-
Excel Schema (Combined Outcomes)sdd-configuration.mdCombined Outcomes Excel Configurations-

Testability & QA​

TopicPrimary DocSectionRelated Docs
HTML Attribute Namingstd-ui-testability.mdNomenclature standards-
Menu Element Attributesstd-ui-testability.mdMenu elements-
Table Attributesstd-ui-testability.mdTable identification-
Cell Attributesstd-ui-testability.mdCell identification-
Widget Attributesstd-ui-testability.mdWidget elements-
Filter Attributesstd-ui-testability.mdFilter elements-
Behat Test Infrastructuresdd-testing.mdTesting Stack-
Behat Step Definitionssdd-testing.mdAvailable Step Definitions-
Gherkin Syntaxsdd-testing.mdGherkin Syntax Reference-
Feature Tagssdd-testing.mdFeature Tags-

Standards & References​

TopicPrimary DocSectionRelated Docs
IEEE 1016-1998 SDD Templatesdd-references.mdSDD Template (TBC)-
SOLID Principlessdd-references.mdCoding standards - SOLID Principle-
MVC Architecturesdd-references.mdMVC Architecture-
Test-Driven Developmentsdd-references.mdTest-Driven Development-
Vue Style Guidesdd-references.mdVue Style Guide Line-
PHP PSR Standardssdd-references.mdPHP PSR Code Style-
UI Design (Figma)sdd-references.mdLook and feel (UI)-

Full Table of Contents​

sdd-architecture.md​

  1. Product design
  2. Context
    • 2.1 Purpose of the System
    • 2.2 System Architecture
    • 2.3 Key features of PCR.AI System
  3. Workflow using PCR.AI System
  4. Architecture Patterns (NEW)
    • 4.1 Domain-Driven Design (DDD) Elements
    • 4.2 Repository Pattern
    • 4.3 Strategy Pattern
    • 4.4 Factory Pattern
    • 4.5 Analysis Flow (6-Stage Pipeline)
  5. AWS Services Summary
  6. AWS Lambda
  7. Amazon Cognito
  8. Amazon ElastiCache
  9. Amazon RDS with Amazon Aurora Serverless v2
  10. Amazon S3
  11. Amazon Simple Queue Service
  12. Amazon Simple Email Service
  13. Amazon DynamoDB
  14. Pusher
  15. Server Database Type Migration
    • 15.1 Two Possible Solutions
  16. Vue Component Architecture
  17. High-Level Entity Relationship Diagram
  18. Well State Model
  19. Complete Database Schema Inventory
  20. Audit Trail System
  21. External Integrations Inventory
  22. Related SRS Requirements

sdd-algorithms.md​

  1. Overview
  2. Running Rules Architecture
  3. Run Import Process
    • 3.1 Use Case Action Explanations
    • 3.2 Validate Run file
    • 3.3 Parse Run File using Parser API
    • 3.4 Convert to standard JSON format
    • 3.5 Analyse Run File
    • 3.6 Store Run File
  4. Curve Alignment Algorithm (NEW)
    • 4.1 Scientific Purpose
    • 4.2 Baseline Calculation Formula
    • 4.3 Alignment Activation Rules
  5. Run Analysis
  6. Configuration Upload Algorithm
    • 6.1 Validate Configuration File
  7. Configuration Export Algorithm
  8. Combined Outcomes Algorithm
  9. Error Code Generation System
  10. Run Status Calculation
  11. Complex Functionality - Rules Engine
    • 11.1 Rules Introduction
    • 11.2 Rule application
    • 11.3 Data validation
    • 11.4 Error detection and notification
    • 11.5 Action and resolution
    • 11.6 Reporting and compliance
  12. Westgard Rules
    • 12.1 1:2S rule
    • 12.2 1:3S rule
    • 12.3 2:2S rule
    • 12.4 7T rule
    • 12.5 Westgard in error
  13. Rule Mapping Architecture
  14. Data Flow Diagrams
  15. Control Flow Diagram
  16. Process Priority Table
  17. Real-Time Event Broadcasting (Pusher)
  18. Asynchronous Job Processing
  19. Trends Report Data Caching (NEW)
    • 19.1 Daily Outcomes Materialized Cache
    • 19.2 Query Algorithm
    • 19.3 Trends Report Alerts
  20. Feature Import/Cascade System (NEW)
    • 20.1 Architecture
    • 20.2 Validation Rules
    • 20.3 Cascade Disable Pattern
    • 20.4 Import Process Flow
  21. Role Alias to Role Workflow (NEW)
    • 21.1 Entry Points
    • 21.2 Transactional Workflow
    • 21.3 Data Dependencies
  22. Developer Documentation Cross-References
  23. Related SRS Requirements

sdd-configuration.md​

  1. Back end configurations
  2. Environment Variables
    • 2.1 PcrAI Environment Variable
    • 2.2 Vapor Environment Variables
    • 2.3 Vapor Secrets
  3. Client Configuration
  4. Control Labels Configurations
  5. Combined Outcomes Excel Configurations
  6. Alerts Configurations
  7. Cross Contamination Limits Configurations
  8. Curve Control Limits Configurations
  9. Delta CT Configurations
  10. Error Codes Configurations
  11. Error Resolutions Configurations
  12. Extractions Configurations
  13. Features Configurations
  14. Help Items Configurations
  15. Known Quantities Configurations
  16. Lims Exports Configurations
  17. Mix and Targets Configurations
  18. QIR - Quantification Settings Configurations
  19. Qualitative Reportings Configurations
  20. Rules Mapping Configurations
  21. Test Codes Configurations
  22. Thermocyclers Configurations
  23. Westgard Limits Configurations
  24. Dyes Configurations
  25. Roles Configurations
  26. Rules Configurations
  27. Westgard Events Configurations
  28. Specimens Configurations
  29. Related SRS Requirements

sdd-deployment-operations.md​

  1. Vapor Configuration
    • 1.1 Vapor Secret in Deployment Console Project
  2. Cognito User Pool Setup
    • 2.1 Process for setting up new Cognito user pools
  3. Environment URL Changes
    • 3.1 Update the Deployment
    • 3.2 Update Cloudflare Certificate
    • 3.3 Update Cognito references
    • 3.4 Update Laravel Environment Variables
  4. Related SRS Requirements

sdd-security.md​

  1. AWS Programmatic Access Key Privileges
  2. Authentication and Authorisation (Cognito based)
    • 2.1 Introduction
    • 2.2 Scope & Intended audience
    • 2.3 Services described
    • 2.4 Architecture (Flowchart)
  3. Authentication Token Architecture (NEW)
    • 3.1 Authentication Flow
    • 3.2 Token Types
    • 3.3 Token Refresh Mechanism
    • 3.4 Session Management
  4. Authentication Middleware (NEW)
    • 4.1 Global Middleware Stack
    • 4.2 Web Middleware Group
    • 4.3 Route Middleware
    • 4.4 Authentication Guards
    • 4.5 Security Headers
    • 4.6 Rate Limiting
    • 4.7 IP-Based Access Control
    • 4.8 AI Security Middleware
  5. AI Prompt Injection Prevention (NEW)
    • 5.1 Input Sanitization
    • 5.2 Input Validation
    • 5.3 Suspicious Pattern Detection
    • 5.4 Enhanced System Instructions
    • 5.5 Rate Limiting
    • 5.6 Request Size Validation
    • 5.7 Suspicious Header Detection
    • 5.8 Comprehensive Logging
    • 5.9 Attack Response Workflow
  6. Related SRS Requirements

std-ui-testability.md (migrated to STD)​

Note: This content was migrated from SDD to STD (Software Test Description) on 2026-01-18.

  1. HTML Attributes
    • 1.1 Nomenclature standards
    • 1.2 Menu element attributes
    • 1.3 Table attributes
    • 1.4 Cell attributes
    • 1.5 Widget attributes
    • 1.6 Filter attributes
  2. Related SRS Requirements

See: ../std/std-ui-testability.md

sdd-testing.md​

  1. Overview
    • 1.1 Testing Stack
    • 1.2 Context Classes
  2. Guidelines for Using Behat Successfully
  3. Gherkin Syntax Reference
    • 3.1 Feature File Structure
    • 3.2 Jira Integration Notes
    • 3.3 Using Datasets
    • 3.4 Using Files
  4. Available Step Definitions
    • 4.1 Configuration Steps
    • 4.2 Run File Steps
    • 4.3 Well Edit Step
    • 4.4 Resolution Steps
    • 4.5 Well Assertion Steps
    • 4.6 Observation Assertion Steps
  5. Feature Tags
  6. Test Repetition Guidelines
  7. Execution
  8. File Structure
  9. Traceability

sdd-references.md​

  1. SDD Template (TBC)
    • 1.1 Authorization
    • 1.2 Table of Changes
    • 1.3 Table Of Contents
    • 1.4 Introduction (Purpose, Scope, Definitions)
    • 1.5 References
    • 1.6 Decomposition Description
    • 1.7 Dependency Description
    • 1.8 Interface Description
    • 1.9 Detailed Design
    • 1.10 Appendices
  2. Completing the SDD - notes
  3. Coding standards (principles) & guide
    • 3.1 SOLID Principle
    • 3.2 MVC Architecture
    • 3.3 Test-Driven Development
    • 3.4 Vue Style Guide Line
    • 3.5 PHP PSR Code Style
  4. Look and feel (UI)

Incomplete Sections Index​

DocumentSectionGap TypeResolverPriority
sdd-architecture.mdHigh Level Use Case DiagramsDECISIONProduct/QALow
sdd-architecture.mdSequence DiagramsDECISIONProduct/QALow
sdd-architecture.mdState DiagramsDECISIONProduct/QALow
sdd-architecture.mdHigh Level ERDDECISIONProduct/QALow
sdd-architecture.mdApplication Feasibility TestDECISIONTech LeadLow
sdd-architecture.mdCost AnalysisDECISIONTech LeadLow
sdd-references.mdPurpose (PCRI-specific)STRUCTURALTechnical WriterHigh
sdd-references.mdScope (PCRI-specific)STRUCTURALTechnical WriterHigh
sdd-references.mdDefinitions (PCRI terms)EXPLANATORYTechnical WriterMedium
sdd-references.mdGUI architectureEXPLANATORYDeveloperMedium
(Missing)Concurrent Process DecompositionSTRUCTURALDeveloperHigh
(Missing)Interprocess DependenciesIMPLEMENTATIONDeveloperHigh
(Missing)Data DependenciesIMPLEMENTATIONDeveloperHigh

SRS Traceability Quick Reference​

SRS DomainPrimary SDDSecondary SDDCoverage
User Managementsdd-security.mdsdd-architecture.md, sdd-deployment-operations.mdHigh
File Importsdd-algorithms.mdsdd-architecture.mdFull
Upload Runssdd-algorithms.mdsdd-architecture.mdFull
Config I/Osdd-algorithms.mdsdd-configuration.mdFull
Kit Configurationsdd-configuration.mdsdd-algorithms.mdFull
Client Configurationsdd-configuration.mdsdd-deployment-operations.mdFull
Rules Enginesdd-algorithms.mdsdd-configuration.mdFull
Combined Outcomessdd-algorithms.mdsdd-configuration.mdFull
Westgardsdd-algorithms.mdsdd-configuration.mdFull
Runfile Reportstd-ui-testability.md-Partial
Tablesstd-ui-testability.md-Partial
Filtersstd-ui-testability.md-Partial
Site Managementsdd-architecture.mdsdd-deployment-operations.mdFull
Notificationssdd-architecture.md-Partial
Audit Logsdd-architecture.mdsdd-security.mdPartial
Analyticssdd-architecture.md-Partial
Non-Functionalsdd-architecture.mdstd-ui-testability.mdFull
Global UIsdd-security.md-Partial
Reanalyzesdd-algorithms.md-Partial
Analyzersdd-algorithms.md-Partial
Reportssdd-configuration.md-Partial

Requirements Coverage Summary​

SDD DocumentRequirements TracedDomains Covered
sdd-architecture.md228
sdd-algorithms.md298
sdd-configuration.md163
sdd-deployment-operations.md74
sdd-security.md93
std-ui-testability.md74
TOTAL9020 domains

See sdd-glossary.md for full terminology (127 terms).

Key Terms​

TermDefinition
CT (Cycle Threshold)The cycle number at which fluorescence exceeds threshold in PCR
CLS (Classification)Result classification for an observation (Positive, Negative, etc.)
MixCombination of targets/dyes that constitute an assay
ObservationData point for a specific target/dye combination in a well
Rule MappingAssignment of rules to specific target/role/specimen combinations
Run FileData file exported from thermocycler instrument
TargetSpecific DNA/RNA sequence detected by the assay
WellSingle reaction location on a PCR plate (e.g., A1-H12)
WestgardStatistical QC rules for control evaluation
SD (Standard Deviation)Statistical dispersion measure for Westgard calculations
IC (Internal Control)Target used to verify extraction and amplification success
LIMSLaboratory Information Management System
DXAIExternal analysis service for curve classification
VaporLaravel deployment platform for AWS Lambda

Key Acronyms​

AcronymExpansion
APIApplication Programming Interface
AWSAmazon Web Services
JWTJSON Web Token
MFAMulti-Factor Authentication
PCRPolymerase Chain Reaction
QCQuality Control
RFURelative Fluorescence Units
SAMLSecurity Assertion Markup Language
SDDSoftware Design Document
SRSSoftware Requirements Specification

IEEE 1016-1998 Compliance Summary​

IEEE ChapterPrimary SDD LocationCompletenessChange
1. Introductionsdd-references.md75%-
2. Referencessdd-references.md100%-
3. Decompositionsdd-architecture.md, sdd-configuration.md95%+10% (Architecture Patterns: DDD, Repository, Strategy, Factory)
4. Dependencysdd-algorithms.md67%+34% (Data Flow Diagrams, Control Flow, Process Priority)
5. Interfacesdd-architecture.md, sdd-deployment-operations.md, sdd-security.md92%+9% (Authentication Middleware, AI Security, Security Headers)
6. Detailed Designsdd-algorithms.md100%- (Curve Alignment, Trends Caching, Feature Import, Role Alias added)
7. AppendicesAll SDD files (traceability sections)100%-

Overall Compliance: 88% (was 78%)

Key Improvements (2026-01-19 Migration):

  • Architecture Patterns: Added DDD elements, Repository/Strategy/Factory patterns, 6-stage analysis pipeline
  • Security Design: Expanded from 77 to 446 lines with AI prompt injection prevention, middleware inventory, security headers
  • Algorithm Design: Expanded from 780 to 1944 lines with curve alignment, trends caching, feature import cascade, role alias workflow
  • Dependency Documentation: Added data flow diagrams, control flow, queue configuration

Review artifacts (gap analysis, compliance audit details) available in output/sdd/review/ for internal use.

Document Relationships Diagram​

                           +------------------+
                           | sdd-references   |
                           | (IEEE Template)  |
                           +--------+---------+
                                    |
          +-------------------------+-------------------------+
          |                         |                         |
+---------v---------+    +----------v----------+    +---------v---------+
| sdd-architecture  |    | sdd-algorithms      |    | sdd-configuration |
| (AWS Components)  |<-->| (Rules & Workflows) |<-->| (Settings)        |
+---------+---------+    +----------+----------+    +---------+---------+
          |                         |                         |
          |              +----------v----------+              |
          |              | std-ui-testability  |              |
          |              | (QA Attributes/STD) |              |
          |              +---------------------+              |
          |                                                   |
+---------v---------+                              +----------v---------+
| sdd-security      |                              | sdd-deployment-ops |
| (Auth Flow)       |<---------------------------->| (Setup Procedures) |
+-------------------+                              +--------------------+

Master Index Version: 1.2 Generated: 2026-01-18 Updated: 2026-01-19 (Code docs migration: AI security, architecture patterns, algorithms) Based on: SDD content files, IEEE compliance audit, code/docs migration, and glossary analysis