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Agentic-RagBot / QUICKSTART.md

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Quick Start Guide - RagBot

Get up and running in 5 minutes!

Step 1: Prerequisites

Before you begin, ensure you have:

Python 3.11+ installed (Download)
Git installed (Download)
FREE API Key from one of:
- Groq - Recommended (Fast & Free)
- Google Gemini - Alternative

System Requirements:

4GB+ RAM
2GB free disk space
No GPU required

Step 2: Installation

Clone the Repository

git clone https://github.com/yourusername/RagBot.git
cd RagBot

Create Virtual Environment

macOS/Linux:

python3 -m venv .venv
source .venv/bin/activate

Windows:

python -m venv .venv
.venv\Scripts\activate

Install Dependencies

pip install -r requirements.txt

⏱️ Takes about 2-3 minutes

Step 3: Configuration

Copy Environment Template

cp .env.template .env

Add Your API Keys

Open .env in your text editor and fill in:

Option 1: Groq (Recommended)

GROQ_API_KEY="your_groq_api_key_here"
LLM_PROVIDER="groq"
EMBEDDING_PROVIDER="google"
GOOGLE_API_KEY="your_google_api_key_here"  # For embeddings

Option 2: Google Gemini Only

GOOGLE_API_KEY="your_google_api_key_here"
LLM_PROVIDER="gemini"
EMBEDDING_PROVIDER="google"

How to get API keys:

Groq API Key (FREE):
- Go to https://console.groq.com/keys
- Sign up (free)
- Click "Create API Key"
- Copy and paste into .env
Google Gemini Key (FREE):
- Go to https://aistudio.google.com/app/apikey
- Sign in with Google account
- Click "Create API Key"
- Copy and paste into .env

Step 4: Verify Installation

Quick system check:

python -c "
from src.workflow import create_guild
print('Testing system...')
guild = create_guild()
print('✅ Success! System ready to use!')
"

If you see "✅ Success!" you're good to go!

Step 5: Run Your First Analysis

Interactive Chat Mode

python scripts/chat.py

Try the example:

You: example

The system will analyze a sample diabetes case and show you the full capabilities.

Try your own input:

You: My glucose is 185, HbA1c is 8.2, and cholesterol is 210

Common Commands

Chat Interface

# Start interactive chat
python scripts/chat.py

# Commands within chat:
example    # Run demo case
help       # Show all biomarkers
quit       # Exit

Python API

from src.workflow import create_guild

# Create the guild
guild = create_guild()

# Analyze biomarkers
result = guild.run({
    "biomarkers": {"Glucose": 185, "HbA1c": 8.2},
    "model_prediction": {"disease": "Diabetes", "confidence": 0.87},
    "patient_context": {"age": 52, "gender": "male"}
})

print(result)

REST API (Optional)

# Start API server
cd api
python -m uvicorn app.main:app --reload

# Access API docs
# Open browser: http://localhost:8000/docs

Troubleshooting

Import Error: "No module named 'langchain'"

Solution: Ensure virtual environment is activated and dependencies installed

source .venv/bin/activate  # or .venv\Scripts\activate on Windows
pip install -r requirements.txt

Error: "GROQ_API_KEY not found"

Solution: Check your .env file exists and has the correct API key

cat .env  # macOS/Linux
type .env  # Windows

# Should show:
# GROQ_API_KEY="gsk_..."

Error: "Vector store not found"

Solution: The vector store will auto-load from existing files. If missing:

# The system will create it automatically on first use
# Or manually by running:
python src/pdf_processor.py

System is slow

Tips:

Use Groq instead of Gemini (faster)
Ensure good internet connection (API calls)
Close unnecessary applications to free RAM

API Key is Invalid

Solution:

Double-check you copied the full key (no extra spaces)
Ensure key hasn't expired
Try generating a new key
Check API provider's status page

Next Steps

Learn More

Full Documentation - Complete system overview
API Guide - REST API documentation
Contributing - How to contribute
Architecture - Deep dive into system design

Customize

Biomarker Validation: Edit config/biomarker_references.json
System Behavior: Modify src/config.py
Agent Logic: Explore src/agents/

Run Tests

# Run unit tests (30 tests, no API keys needed)
.venv\Scripts\python.exe -m pytest tests/ -q \
  --ignore=tests/test_basic.py \
  --ignore=tests/test_diabetes_patient.py \
  --ignore=tests/test_evolution_loop.py \
  --ignore=tests/test_evolution_quick.py \
  --ignore=tests/test_evaluation_system.py

# Run integration tests (requires Groq/Gemini API key)
.venv\Scripts\python.exe -m pytest tests/test_diabetes_patient.py -v

Example Session

$ python scripts/chat.py

======================================================================
RagBot - Interactive Chat
======================================================================

You can:
  1. Describe your biomarkers (e.g., 'My glucose is 140, HbA1c is 7.5')
  2. Type 'example' to see a sample diabetes case
  3. Type 'help' for biomarker list
  4. Type 'quit' to exit

🔧 Initializing medical knowledge system...
✓ System ready!

You: My glucose is 185 and HbA1c is 8.2

🔍 Analyzing your input...
✅ Found 2 biomarkers: Glucose, HbA1c
🧠 Predicting likely condition...
✅ Predicted: Diabetes (87% confidence)
📚 Consulting medical knowledge base...

🤖 RAG-BOT:
Hi there! 👋

Based on your biomarkers, I've analyzed your results:

🔴 PRIMARY FINDING: Type 2 Diabetes (87% confidence)

📊 YOUR BIOMARKERS:
├─ Glucose: 185 mg/dL [HIGH] (Normal: 70-100)
└─ HbA1c: 8.2% [CRITICAL HIGH] (Normal: <5.7)

🔬 WHAT THIS MEANS:
Your elevated glucose and HbA1c indicate Type 2 Diabetes...
[continues with full analysis]

Getting Help

Issues: GitHub Issues
Discussions: GitHub Discussions
Documentation: Check the docs/ folder

Quick Reference Card

┌─────────────────────────────────────────────────────────┐
│               RagBot Cheat Sheet                    │
├─────────────────────────────────────────────────────────┤
│ START CHAT:  python scripts/chat.py                    │
│ START API:   cd api && uvicorn app.main:app --reload   │
│ RUN TESTS:   pytest                                     │
│ FORMAT CODE: black src/                                 │
├─────────────────────────────────────────────────────────┤
│ CHAT COMMANDS:                                          │
│   example  - Demo diabetes case                         │
│   help     - List biomarkers                            │
│   quit     - Exit                                       │
├─────────────────────────────────────────────────────────┤
│ SUPPORTED BIOMARKERS: 24 total                          │
│   Glucose, HbA1c, Cholesterol, LDL Cholesterol,    │
│   HDL Cholesterol, Triglycerides, Hemoglobin,       │
│   Platelets, White Blood Cells, Red Blood Cells,    │
│   BMI, Systolic Blood Pressure, and more...          │
├─────────────────────────────────────────────────────────┤
│ DETECTED DISEASES: 5 types                              │
│   Diabetes, Anemia, Heart Disease,                      │
│   Thalassemia, Thrombocytopenia                         │
└─────────────────────────────────────────────────────────┘

Ready to analyze biomarkers? Let's go!