Introduction

OpenSpecimen follows a modular, service-oriented architecture comprising three main layers:

• Frontend (UI): User-facing web interface for data entry and management.

• Backend (API): RESTful services implementing business logic.

• Database: Central repository for metadata and audit logs.

Technology Stack: Java (Spring), Hibernate, Oracle/MySQL, REST APIs, VueJS (for UI).

Backend Architecture

• Built using Java and the Spring Framework.

• Follows a layered approach with Controller, Service, and DAO layers.

• Business logic is exposed via RESTful APIs.

• Uses Hibernate ORM for database interaction.

• Supports modular plugins to extend core functionality without modifying base code.

• Can be distributed across multiple servers for high availability.

Frontend Architecture

• Implemented using VueJS for a responsive, single-page application experience.

• Communicates with backend via REST APIs.

• Uses reusable components and services for better maintainability.

Database Layer

• Supports Oracle and MySQL databases.

• Designed with normalized schema for flexibility and performance.

• Tracks all entity changes via audit tables.

Security and Authentication

• Implements role-based access control (RBAC).

• Supports LDAP, Active Directory, and OAuth2 authentication.

• Uses HTTPS for secure data transmission.

• Maintains audit logs for all user actions.

Customisation and Extensibility

• The plugin framework allows new features without altering the core code.

• Supports custom forms, workflows, and reports.

Network Diagram

Notes:

• This diagram depicts OpenSpecimen configuration for one environment. The same is replicated if there are multiple environments (e.g. test, production, etc).

• This diagram does not include any integration components. E.g., automated freezers, EPIC, REDCap, etc. Refer to individual architecture documents for each integration.

Software Requirements

Others

• SMTP server details

• SAML/LDAP details to integrate with the institution's user account

• SSL certificate for Apache

• Domain name for OpenSpecimen (e.g. openspecimen.yourinstitute.edu)

• Service account for VMs

Hardware Requirements

User Access

Sudo Access Details

1. Install OpenSpecimen as a service using systemctl (RHEL lineage) / service (Debian lineage) commands.

2. Restart OpenSpecimen service.

3. Configure and restart the Apache webserver.

4. Configure and restart database server (Oracle / MySQL)

5. Configure and restart MTA like Postfix. Optional. Required only if an intermediate MTA is used.

6. Create/update cronjobs