Architecture & Deployment

Architecture Overview

                        ┌─────────────────────────┐
                        │      INTERNET            │
                        │   app.discoverant.com    │
                        └────────────┬────────────┘
                                     │ :443 TLS
                        ┌────────────▼────────────┐
                        │     Nginx  (Gateway)     │
                        │     adroit-nginx :80     │
                        └──┬─────────────────┬────┘
                           │                 │
                   /app/*  │                 │  /api/*
                           │                 │
              ┌────────────▼──┐    ┌────────▼──────────┐
              │   Frontend    │    │     Backend        │
              │   React/TS    │    │   FastAPI/Python   │
              │   :3100       │    │   :8000            │
              └───────────────┘    └──┬──────────┬─────┘
                                     │          │
                          ┌──────────▼──┐  ┌───▼───────┐
                          │  PgBouncer  │  │   Redis    │
                          │  :6432      │  │   :6379    │
                          └──────┬──────┘  └───────────┘
                                 │
                       ┌─────────▼──────────┐
                       │    PostgreSQL 16    │
                       │    + Bingo Cart.    │
                       │    :5432            │
                       │                    │
                       │  88 GB / 174M rows │
                       └────────────────────┘

Docker Containers

Nginx Routing Rules

The gateway nginx instance handles all inbound traffic for app.discoverant.com:

Proxy Configuration

resolver 127.0.0.11;          # Docker embedded DNS
set $backend http://backend:8000;  # Variable to avoid stale DNS caching
set $frontend http://frontend:3100;

location /api/ {
    proxy_pass $backend;       # No trailing URI — preserves original path
    proxy_set_header Host $host;
    proxy_set_header X-Real-IP $remote_addr;
}

Important: The $backend variable approach with resolver directive prevents nginx from caching DNS at startup. Do NOT use literal hostnames or 172.17.0.1 (wrong Docker network).

Port Map

Data Layer

PostgreSQL 16 + Bingo Cartridge

Primary datastore hosting 88 GB across 174M+ rows. The EPAM Bingo cartridge provides chemical-aware indexing for substructure and similarity search directly in SQL.

• Database: adroit_chemistry
• Bingo functions: bingo.searchSub(), bingo.searchSim(), bingo.checkMolecule()
• Bingo indexes on patent_chem.surechembl_compounds, compounds.pubchem, compounds.chembl
• Full ECFP4 fingerprint-based Tanimoto similarity at the SQL level

Redis

• Session token cache
• Background task queue (patent collision, enrichment jobs)
• Temporary result storage for long-running analyses

PgBouncer

• Connection pooling to manage concurrent database connections
• Transaction-mode pooling for short-lived API queries
• Prevents PostgreSQL connection exhaustion under load

Security Model

Authentication Flow

1. User logs in via /api/v1/auth/login
2. Backend validates credentials against local database
3. JWT issued (HS256, signed with app secret)
4. Frontend stores token in localStorage, sends as Authorization: Bearer
5. Every API endpoint validates token via get_current_user dependency

Tenant Isolation

• All user data is scoped by tenant_id
• Molecules, reactions, projects, files — all tenant-filtered at query level
• No cross-tenant data leakage possible through API

Filesystem Isolation

• Uploaded files stored in tenant-scoped directories
• File paths validated to prevent directory traversal
• Docker volumes isolate container filesystems

Deployment Process

Frontend

# Build and deploy (requires rebuild for changes)
docker compose build frontend
docker compose up -d frontend

Backend

The backend uses Uvicorn with WatchFiles — code changes are automatically detected and reloaded. No rebuild required for Python changes.

# Only needed for dependency changes
docker compose build backend
docker compose up -d backend

Database Migrations

# Copy SQL into container, then execute
docker cp migration.sql adroit-postgres:/tmp/
docker exec -i adroit-postgres psql -U adroit_user -d adroit_chemistry -f /tmp/migration.sql

Server Specification