%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#4A90D9', 'primaryTextColor': '#fff', 'primaryBorderColor': '#2C5F8A', 'lineColor': '#666', 'secondaryColor': '#52B788', 'tertiaryColor': '#F8F9FA'}}}%%
graph TB
    subgraph Clients["🖥️ Client Layer"]
        CD["🤖 Claude Desktop"]
        VS["💻 VS Code / Cursor"]
        CC["🔗 Custom MCP Clients"]
    end

    subgraph Gateway["🌐 API Gateway Layer"]
        MCP_EP["⚡ MCP Endpoint\n/mcp"]
        NLQ_EP["🔍 NLQ Endpoint\n/nlq"]
        GE_EP["📊 Graph Explorer\n/graph"]
        HE["💚 Health Check\n/health"]
    end

    subgraph Core["🧠 Core Application Layer"]
        direction TB
        GTP["🔄 GoT Processor\nOrchestrator"]
        subgraph Pipeline["ASR-GoT 8-Stage Pipeline"]
            S1["1️⃣ Init &\nContext Setup"]
            S2["2️⃣ Query\nDecomposition"]
            S3["3️⃣ Hypothesis\nGeneration"]
            S4["4️⃣ Evidence\nIntegration"]
            S5["5️⃣ Pruning &\nMerging"]
            S6["6️⃣ Subgraph\nExtraction"]
            S7["7️⃣ Synthesis &\nComposition"]
            S8["8️⃣ Reflection &\nAudit"]
            S1 --> S2 --> S3 --> S4 --> S5 --> S6 --> S7 --> S8
        end
        GTP --> Pipeline
    end

    subgraph Services["🛠️ Service Layer"]
        LLM["🤖 LLM Service\nOpenAI / Claude"]
        EDB["📚 Evidence DB\nPubMed · Scholar · Exa"]
    end

    subgraph Storage["🗄️ Storage Layer"]
        NEO4J["📦 Neo4j\nGraph Database"]
        CONFIG["⚙️ Config\n(YAML + ENV)"]
    end

    Clients -->|"MCP JSON-RPC\nBearer Auth"| Gateway
    MCP_EP --> GTP
    NLQ_EP --> LLM
    GE_EP --> NEO4J
    GTP --> Services
    GTP --> NEO4J
    LLM --> EDB

    style Clients fill:#E3F2FD,stroke:#1565C0
    style Gateway fill:#F3E5F5,stroke:#6A1B9A
    style Core fill:#E8F5E9,stroke:#1B5E20
    style Services fill:#FFF8E1,stroke:#F57F17
    style Storage fill:#FCE4EC,stroke:#880E4F

%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#7B68EE', 'edgeLabelBackground': '#fff'}}}%%
flowchart LR
    Q([❓ Scientific\nQuestion]) --> S1

    subgraph S1["Stage 1: Initialization"]
        I1["Set context\n& parameters"]
        I2["Create root\ngraph node"]
        I1 --> I2
    end

    subgraph S2["Stage 2: Decomposition"]
        D1["Identify\nsub-questions"]
        D2["Map knowledge\ndomains"]
        D1 --> D2
    end

    subgraph S3["Stage 3: Hypothesis"]
        H1["Generate\nhypotheses"]
        H2["Score initial\nconfidence"]
        H1 --> H2
    end

    subgraph S4["Stage 4: Evidence"]
        E1["Query PubMed\nScholar · Exa"]
        E2["Integrate\nevidence nodes"]
        E1 --> E2
    end

    subgraph S5["Stage 5: Pruning"]
        P1["Remove weak\nhypotheses"]
        P2["Merge related\nnodes"]
        P1 --> P2
    end

    subgraph S6["Stage 6: Subgraph"]
        SG1["Extract key\nsubgraphs"]
        SG2["Score relevance\n& centrality"]
        SG1 --> SG2
    end

    subgraph S7["Stage 7: Synthesis"]
        C1["Compose final\nnarrative"]
        C2["Build\nconclusions"]
        C1 --> C2
    end

    subgraph S8["Stage 8: Reflection"]
        R1["Audit\nconsistency"]
        R2["Return final\nresult"]
        R1 --> R2
    end

    S1 --> S2 --> S3 --> S4 --> S5 --> S6 --> S7 --> S8
    S8 --> A([✅ Reasoned\nAnswer])

    style Q fill:#FFD700,stroke:#DAA520,color:#000
    style A fill:#90EE90,stroke:#228B22,color:#000

%%{init: {'theme': 'base', 'themeVariables': {'primaryColor': '#6C63FF', 'primaryTextColor': '#fff', 'edgeLabelBackground': '#f0f0ff'}}}%%
graph TD
    RootQuery["🔍 Root Query\n(Session Node)"]

    subgraph Decomp["📐 Decomposition Layer"]
        D1["📌 Sub-question A\n[domain: biology]"]
        D2["📌 Sub-question B\n[domain: chemistry]"]
        D3["📌 Sub-question C\n[domain: physics]"]
    end

    subgraph Hypo["💡 Hypothesis Layer"]
        H1["💭 Hypothesis 1\nconf: 0.85"]
        H2["💭 Hypothesis 2\nconf: 0.72"]
        H3["💭 Hypothesis 3\nconf: 0.61"]
        H4["💭 Hypothesis 4\nconf: 0.90"]
    end

    subgraph Evid["🔬 Evidence Layer"]
        E1["📄 PubMed Paper\nPMID: 38492"]
        E2["📄 Scholar Article\nDOI: 10.1038/..."]
        E3["🌐 Exa Result\nexpert consensus"]
        E4["📊 Statistical\nMeta-analysis"]
    end

    subgraph Synth["🎯 Synthesis Layer"]
        C1["✅ Merged\nConclusion A"]
        C2["✅ Merged\nConclusion B"]
        FINAL["🏆 Final Answer\n[confidence: 0.88]"]
    end

    RootQuery -->|"DECOMPOSES_TO"| D1
    RootQuery -->|"DECOMPOSES_TO"| D2
    RootQuery -->|"DECOMPOSES_TO"| D3

    D1 -->|"GENERATES"| H1
    D1 -->|"GENERATES"| H2
    D2 -->|"GENERATES"| H3
    D3 -->|"GENERATES"| H4

    H1 -->|"SUPPORTED_BY"| E1
    H2 -->|"SUPPORTED_BY"| E2
    H3 -->|"CONTRADICTED_BY"| E3
    H4 -->|"SUPPORTED_BY"| E4

    H1 -->|"MERGES_WITH"| C1
    H4 -->|"MERGES_WITH"| C1
    H2 -->|"MERGES_WITH"| C2
    C1 -->|"SYNTHESIZES_TO"| FINAL
    C2 -->|"SYNTHESIZES_TO"| FINAL

    style RootQuery fill:#4A90D9,color:#fff,stroke:#2C5F8A
    style FINAL fill:#27AE60,color:#fff,stroke:#1E8449
    style H3 fill:#E74C3C,color:#fff,stroke:#C0392B

%%{init: {'theme': 'base'}}%%
sequenceDiagram
    actor User as 🤖 Claude / MCP Client
    participant API as ⚡ FastAPI Server
    participant Auth as 🔐 Auth Middleware
    participant GTP as 🧠 GoT Processor
    participant NEO as 📦 Neo4j DB
    participant LLM as 🤖 LLM Service

    User->>API: POST /mcp {"method": "asr_got.query"}
    API->>Auth: Verify Bearer Token
    Auth-->>API: ✅ Authorized

    API->>GTP: Process query
    GTP->>NEO: Create session + root node

    loop 8 Pipeline Stages
        GTP->>LLM: Generate hypotheses / summaries
        LLM-->>GTP: LLM response
        GTP->>NEO: Write nodes & relationships
        NEO-->>GTP: Confirmed
    end

    GTP->>NEO: Extract final subgraph
    NEO-->>GTP: Final answer graph
    GTP-->>API: Structured result

    API-->>User: JSON-RPC response\n{result, confidence, graph_state}

Adaptive-Graph-of-Thoughts-MCP-server/
├── 📁 .github/             # CI/CD workflows (CodeQL, Dependabot)
├── 📁 agt_setup/           # Interactive setup wizard CLI
├── 📁 config/              # settings.yaml configuration
├── 📁 docs_src/            # MkDocs documentation source
├── 📁 helm/                # Kubernetes Helm chart
├── 📁 src/
│   └── 📁 adaptive_graph_of_thoughts/
│       ├── 📁 api/         # FastAPI routes & schemas
│       ├── 📁 application/ # GoTProcessor orchestrator
│       ├── 📁 domain/      # 8-stage pipeline & models
│       ├── 📁 infrastructure/ # Neo4j utilities
│       └── 📁 services/    # LLM & external API clients
├── 📁 tests/               # Comprehensive test suite
├── Dockerfile
├── docker-compose.yml
├── pyproject.toml
└── README.md

git clone https://github.com/SaptaDey/Adaptive-Graph-of-Thoughts-MCP-server.git
cd Adaptive-Graph-of-Thoughts-MCP-server
poetry install
poetry run python -m agt_setup   # Interactive credential setup wizard
poetry run uvicorn adaptive_graph_of_thoughts.main:app --reload

git clone https://github.com/SaptaDey/Adaptive-Graph-of-Thoughts-MCP-server.git
   cd Adaptive-Graph-of-Thoughts-MCP-server

poetry install

poetry shell

# Copy example configuration
   cp config/settings.example.yaml config/settings.yaml
   
   # Edit configuration as needed
   vim config/settings.yaml

# Create .env file for sensitive configuration
   echo "LOG_LEVEL=DEBUG" > .env
   echo "API_HOST=0.0.0.0" >> .env
   echo "API_PORT=8000" >> .env

python src/adaptive_graph_of_thoughts/main.py

uvicorn adaptive_graph_of_thoughts.main:app --reload --host 0.0.0.0 --port 8000

poetry run python -m agt_setup

graph TB
    subgraph "Development Environment"
        A[👨‍💻 Developer] --> B[🐳 Docker Compose]
    end
    
    subgraph "Container Orchestration"
        B --> C[📦 Adaptive Graph of Thoughts Container]
        B --> D[📊 Monitoring Container]
        B --> E[🗄️ Database Container]
    end
    
    subgraph "Adaptive Graph of Thoughts Application"
        C --> F[⚡ FastAPI Server]
        F --> G[🧠 ASR-GoT Engine]
        F --> H[🔌 MCP Protocol]
    end
    
    subgraph "External Integrations"
        H --> I[🤖 Claude Desktop]
        H --> J[🔗 Other AI Clients]
    end
    
    style A fill:#e1f5fe
    style B fill:#f3e5f5
    style C fill:#e8f5e8
    style F fill:#fff3e0
    style G fill:#ffebee
    style H fill:#f1f8e9

# Build and run all services
   docker-compose up --build
   
   # For detached mode (background)
   docker-compose up --build -d
   
   # View logs
   docker-compose logs -f adaptive-graph-of-thoughts

# Build the image
   docker build -t adaptive-graph-of-thoughts:latest .
   
   # Run the container
   docker run -p 8000:8000 -v $(pwd)/config:/app/config adaptive-graph-of-thoughts:latest

# Use production compose file
   docker-compose -f docker-compose.prod.yml up --build -d

helm install agot helm/agot-server

{
  "mcpServers": {
    "adaptive-graph-of-thoughts": {
      "command": "python",
      "args": ["-m", "adaptive_graph_of_thoughts.main"],
      "cwd": "/path/to/Adaptive-Graph-of-Thoughts-MCP-server",
      "env": {
        "NEO4J_URI": "bolt://localhost:7687",
        "NEO4J_USER": "neo4j",
        "NEO4J_PASSWORD": "your_password",
        "MCP_TRANSPORT_TYPE": "stdio"
      }
    }
  }
}

{
      "jsonrpc": "2.0",
      "method": "asr_got.query",
      "params": {
        "query": "Analyze the relationship between microbiome diversity and cancer progression.",
        "parameters": {
          "include_reasoning_trace": true,
          "include_graph_state": false
        }
      },
      "id": "123"
    }

{
      "status": "healthy",
      "version": "0.1.0" 
    }

# Run full test suite with coverage using Poetry
poetry run pytest --cov=src --cov-report=html --cov-report=term

# Or using Makefile for the default test run
make test

# Run specific test categories (using poetry)
poetry run pytest tests/unit/stages/          # Stage-specific tests
poetry run pytest tests/integration/         # Integration tests
poetry run pytest -k "test_confidence"       # Tests matching pattern

# Type checking and linting (can also be run via Makefile targets: make lint, make check-types)
poetry run mypy src/ --strict                # Strict type checking
poetry run ruff check . --fix                # Auto-fix linting issues
poetry run ruff format .                     # Format code

# Pre-commit hooks (recommended)
poetry run pre-commit install                # Install hooks
poetry run pre-commit run --all-files       # Run all hooks (runs Ruff and MyPy)

# See Makefile for other useful targets like 'make all-checks'.