# Verify database, GPU, and schema integrity
python -m src.cli check-health --smoke-test

# If tables are missing or authentication fails (HTTP 401):
python -m src.cli fix-environment

# Or reset security settings specifically:
python -m src.cli reset-security

# Install dependencies
pip install -r requirements.txt

# Set AWS credentials
export AWS_PROFILE=your-profile

# Configure NV-CLIP endpoint (for medical images and memory)
export NVCLIP_BASE_URL="http://localhost:8002/v1"  # Local NIM via SSH tunnel

# Run the chat app
cd mcp-server
streamlit run streamlit_app.py

# Configure MCP client to point to:
python mcp-server/fhir_graphrag_mcp_server.py

flowchart TB
    subgraph UI["🖥️ Presentation Layer"]
        ST[Streamlit Chat UI<br/>v2.15.0]
    end

    subgraph LLM["🧠 AI/LLM Layer"]
        direction LR
        NIM[NVIDIA NIM<br/>Llama 3.1 8B]
        OAI[OpenAI<br/>GPT-4o]
        BED[AWS Bedrock<br/>Claude Sonnet 4.5]
    end

    subgraph MCP["⚡ MCP Server Layer"]
        MCPS[FHIR + GraphRAG MCP Server<br/>14+ Medical Tools]
    end

    subgraph DATA["🗄️ Data Layer"]
        direction LR
        IRIS[(InterSystems IRIS<br/>Vector Database)]
        FHIR[FHIR Documents<br/>51 Clinical Notes]
        GRAPH[Knowledge Graph<br/>83 Entities • 540 Relations]
        IMG[Medical Images<br/>50 Chest X-rays]
        MEM[Agent Memory<br/>Semantic Store]
    end

    subgraph EMB["🔢 Embedding Layer"]
        NVCLIP[NVIDIA NV-CLIP<br/>1024-dim Multimodal]
    end

    ST <-->|Multi-LLM Support| LLM
    LLM <-->|MCP Protocol| MCPS
    MCPS <-->|IRIS Native API| IRIS
    IRIS --- FHIR
    IRIS --- GRAPH
    IRIS --- IMG
    IRIS --- MEM
    MCPS <-->|Embedding API| NVCLIP

flowchart LR
    subgraph INPUT["📥 Input"]
        Q[User Query]
    end

    subgraph RECALL["🔄 Auto-Recall"]
        MR[Memory Recall<br/>Past Corrections]
    end

    subgraph SEARCH["🔍 Multi-Modal Search"]
        direction TB
        VS[Vector Search<br/>FHIR Documents]
        GS[Graph Search<br/>Entities & Relations]
        IS[Image Search<br/>NV-CLIP Similarity]
    end

    subgraph FUSION["⚗️ Fusion"]
        RRF[Reciprocal Rank Fusion<br/>RRF Algorithm]
    end

    subgraph OUTPUT["📤 Output"]
        R[Ranked Results +<br/>Knowledge Graph Viz]
    end

    Q --> MR
    MR --> VS
    MR --> GS
    MR --> IS
    VS --> RRF
    GS --> RRF
    IS --> RRF
    RRF --> R

sequenceDiagram
    participant U as User
    participant S as Streamlit UI
    participant L as LLM (Claude/GPT/NIM)
    participant M as MCP Server
    participant I as IRIS DB
    participant N as NV-CLIP

    U->>S: "Find pneumonia X-rays"
    S->>L: Query + Tools
    L->>M: search_medical_images()
    M->>N: embed_text(query)
    N-->>M: 1024-dim vector
    M->>I: VECTOR_COSINE search
    I-->>M: Top-K results
    M-->>L: Images + metadata
    L->>M: search_knowledge_graph()
    M->>I: Entity/relation query
    I-->>M: Graph data
    M-->>L: Entities + relations
    L-->>S: Response + visualizations
    S-->>U: Display results

flowchart TB
    subgraph APP["🏥 Medical GraphRAG Assistant"]
        MCP[MCP Server<br/>14+ Medical Tools]
        CFG[YAML Config<br/>CloudConfiguration API]
    end

    subgraph IRIS_PKG["📦 InterSystems IRIS Vector Packages"]
        direction TB
        RAG["<a href='https://pypi.org/project/iris-vector-rag/'>iris-vector-rag</a><br/>RAG Framework"]
        GRAPH["<a href='https://pypi.org/project/iris-vector-graph/'>iris-vector-graph</a><br/>Graph Toolkit"]
        TEST["<a href='https://pypi.org/project/iris-devtester/'>iris-devtester</a><br/>Env Manager"]

        subgraph RAG_DETAIL["iris-vector-rag Features"]
            BYOT[BYOT Storage<br/>Bring Your Own Tables]
            PIPE[RAG Pipelines<br/>basic • graphrag • crag]
            SCHEMA[SchemaManager<br/>Table Validation]
        end

        subgraph GRAPH_DETAIL["iris-vector-graph Features"]
            ENT[Entity Storage<br/>Type-Tagged Nodes]
            REL[Relationship Store<br/>Typed Edges]
            TRAV[Graph Traversal<br/>Path Queries]
        end
    end

    subgraph IRIS_DB["🗄️ InterSystems IRIS"]
        VEC[(VECTOR Column<br/>DOUBLE, 1024)]
        SQL[(SQL Tables<br/>ClinicalNoteVectors)]
        KG[(Knowledge Graph<br/>Entities • Relations)]
    end

    MCP --> RAG
    MCP --> GRAPH
    CFG --> RAG
    RAG --> BYOT
    RAG --> PIPE
    RAG --> SCHEMA
    GRAPH --> ENT
    GRAPH --> REL
    GRAPH --> TRAV
    
    %% The Integration Points
    PIPE -.->|GraphRAG Pipeline| GRAPH
    ENT --> VEC
    
    %% Lifecycle Management
    TEST -.->|Config & Reset| IRIS_DB
    
    BYOT --> VEC
    SCHEMA --> SQL
    ENT --> KG
    REL --> KG

flowchart TB
    subgraph AWS["☁️ AWS EC2 g5.xlarge"]
        subgraph GPU["🎮 NVIDIA A10G GPU (24GB)"]
            direction TB
            NIM_LLM["<a href='https://build.nvidia.com'>NIM Container</a><br/>Port 8001<br/>meta/llama-3.1-8b-instruct"]
            NIM_CLIP["<a href='https://build.nvidia.com/nvidia/nvclip'>NV-CLIP Container</a><br/>Port 8002<br/>nvidia/nvclip"]
        end

        subgraph SERVICES["🔧 Application Services"]
            MCP[MCP Server<br/>Medical Tools]
            ST[Streamlit UI<br/>Port 8501]
            IRIS[(IRIS DB<br/>Port 1972)]
        end
    end

    subgraph CLIENT["💻 Client"]
        TUNNEL[SSH Tunnel<br/>localhost:8002 → AWS:8002]
        APP[Local Development]
    end

    APP --> |NVCLIP_BASE_URL| TUNNEL
    TUNNEL --> NIM_CLIP
    ST --> MCP
    MCP --> |Text Embeddings| NIM_LLM
    MCP --> |Image Embeddings| NIM_CLIP
    MCP --> |Vector Search| IRIS
    NIM_LLM --> GPU
    NIM_CLIP --> GPU

flowchart LR
    subgraph FHIR["📄 FHIR Repository"]
        DOC[DocumentReference<br/>Clinical Notes]
    end

    subgraph EXTRACT["🔬 Entity Extraction"]
        direction TB
        REGEX[Regex Patterns<br/>Confidence-Scored]
        TYPES[Entity Types:<br/>SYMPTOM • CONDITION<br/>MEDICATION • PROCEDURE<br/>BODY_PART • TEMPORAL]
    end

    subgraph RELATE["🔗 Relationship Inference"]
        direction TB
        HEUR[Heuristic Rules:<br/>Proximity + Context]
        REL_TYPES[Relationship Types:<br/>TREATS • CAUSES<br/>LOCATED_IN • CO_OCCURS]
    end

    subgraph STORE["🗄️ Knowledge Graph Tables"]
        ENT_TBL[(RAG.Entities<br/>83 entities)]
        REL_TBL[(RAG.EntityRelationships<br/>540 relationships)]
    end

    DOC --> REGEX
    REGEX --> TYPES
    TYPES --> HEUR
    HEUR --> REL_TYPES
    REL_TYPES --> ENT_TBL
    REL_TYPES --> REL_TBL

flowchart TB
    subgraph LLM["🧠 LLM (Claude/GPT/NIM)"]
        AGENT[Agentic Chat]
    end

    subgraph MCP["⚡ MCP Server Tools"]
        direction TB
        subgraph SEARCH["🔍 Search Tools"]
            T1[search_fhir_documents<br/>Full-text clinical notes]
            T2[search_knowledge_graph<br/>Entity-based search]
            T3[hybrid_search<br/>RRF fusion of all sources]
            T4[search_medical_images<br/>NV-CLIP similarity]
        end

        subgraph DETAIL["📋 Detail Tools"]
            T5[get_document_details<br/>Full document content]
            T6[get_entity_relationships<br/>Graph traversal]
            T7[get_entity_statistics<br/>Graph stats]
        end

        subgraph MEMORY["💾 Memory Tools"]
            T8[remember_information<br/>Store corrections/prefs]
            T9[recall_information<br/>Semantic memory search]
            T10[get_memory_stats<br/>Memory statistics]
        end

        subgraph VIZ["📊 Visualization Tools"]
            T11[plot_symptom_frequency]
            T12[plot_entity_distribution]
            T13[plot_patient_timeline]
            T14[plot_entity_network]
        end
    end

    subgraph DATA["🗄️ Data Sources"]
        FHIR[(FHIR Documents)]
        KG[(Knowledge Graph)]
        IMG[(Medical Images)]
        MEM[(Agent Memory)]
    end

    AGENT -->|MCP Protocol| MCP
    T1 --> FHIR
    T2 --> KG
    T3 --> FHIR
    T3 --> KG
    T3 --> IMG
    T4 --> IMG
    T8 --> MEM
    T9 --> MEM

flowchart LR
    subgraph INGEST["📥 Data Ingestion (Batch)"]
        direction TB
        FHIR_SRC[FHIR Bundles<br/>JSON Resources]
        CXR[MIMIC-CXR<br/>Chest X-rays]
        PARSE[fhirpy Parser<br/>Resource Extraction]
    end

    subgraph EMBED["🔢 Vectorization"]
        direction TB
        NIM_EMB[NVIDIA NIM<br/>NV-EmbedQA-E5-v5]
        NVCLIP_EMB[NV-CLIP<br/>Multimodal 1024-dim]
        NER[Entity Extraction<br/>Symptoms • Conditions]
    end

    subgraph STORE["🗄️ IRIS FHIR Repository"]
        direction TB
        subgraph FHIR_TABLES["FHIR Tables"]
            DOC[(ClinicalNoteVectors<br/>51 Documents)]
            IMG[(MIMICCXRImages<br/>50 X-rays)]
        end
        subgraph GRAPH_TABLES["Knowledge Graph"]
            ENT_TBL[(Entities<br/>83 Nodes)]
            REL_TBL[(EntityRelationships<br/>540 Edges)]
        end
        subgraph MEM_TABLES["Agent Memory"]
            MEM_TBL[(AgentMemoryVectors<br/>Semantic Store)]
        end
    end

    subgraph QUERY["🔍 Query Processing"]
        direction TB
        VEC_SEARCH[Vector Search<br/>VECTOR_COSINE]
        GRAPH_TRAV[Graph Traversal<br/>Entity → Relations]
        RRF_FUSE[RRF Fusion<br/>Rank Combination]
    end

    subgraph OUTPUT["📤 Results"]
        RANKED[Ranked Documents<br/>+ Knowledge Graph]
    end

    FHIR_SRC --> PARSE
    CXR --> NVCLIP_EMB
    PARSE --> NIM_EMB
    PARSE --> NER
    NIM_EMB --> DOC
    NVCLIP_EMB --> IMG
    NER --> ENT_TBL
    NER --> REL_TBL
    DOC --> VEC_SEARCH
    IMG --> VEC_SEARCH
    ENT_TBL --> GRAPH_TRAV
    REL_TBL --> GRAPH_TRAV
    MEM_TBL --> VEC_SEARCH
    VEC_SEARCH --> RRF_FUSE
    GRAPH_TRAV --> RRF_FUSE
    RRF_FUSE --> RANKED

erDiagram
    ClinicalNoteVectors {
        int ID PK
        string ResourceID UK
        string PatientID
        string DocumentType
        text TextContent
        vector Embedding "VECTOR(DOUBLE,1024)"
        string EmbeddingModel
        string SourceBundle
    }

    MIMICCXRImages {
        int ID PK
        string DicomID UK
        string PatientID
        string StudyID
        string ViewPosition
        text Findings
        vector Embedding "VECTOR(DOUBLE,1024)"
        string ImagePath
    }

    Entities {
        int ID PK
        string EntityText
        string EntityType
        float Confidence
        string SourceDocID FK
    }

    EntityRelationships {
        int ID PK
        int SourceEntityID FK
        int TargetEntityID FK
        string RelationType
        float Confidence
        string SourceText
        string TargetText
    }

    AgentMemoryVectors {
        int ID PK
        string MemoryType
        text Content
        vector Embedding "VECTOR(DOUBLE,1024)"
        datetime CreatedAt
    }

    ClinicalNoteVectors ||--o{ Entities : "extracts"
    Entities ||--o{ EntityRelationships : "source"
    Entities ||--o{ EntityRelationships : "target"

# AWS Credentials
export AWS_PROFILE=your-profile  # or set AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY

# IRIS Database (defaults to local Docker container)
export IRIS_HOST=localhost    # Default; set to your EC2 IP for remote
export IRIS_PORT=32782        # Docker port (1972 for native IRIS)
export IRIS_NAMESPACE=%SYS
export IRIS_USERNAME=_SYSTEM
export IRIS_PASSWORD=SYS      # Default Docker password

# NVIDIA NV-CLIP (for medical images and memory)
export NVCLIP_BASE_URL="http://localhost:8002/v1"  # Local NIM via SSH tunnel
# or use cloud API:
# export NVCLIP_BASE_URL="https://integrate.api.nvidia.com/v1"
# export NVIDIA_API_KEY="your-api-key"

medical-graphrag-assistant/
├── mcp-server/                      # MCP server and Streamlit app
│   ├── fhir_graphrag_mcp_server.py  # MCP server (Tool Wrappers)
│   ├── streamlit_app.py             # Chat UI v2.12.0 with memory editor
│   └── test_*.py                    # Integration tests
├── src/
│   ├── cli/                         # System Management CLI
│   ├── db/                          # IRIS database clients
│   ├── embeddings/                  # NVIDIA NIM integration
│   ├── memory/                      # Agent memory system
│   ├── search/                      # Decoupled Search Services (Business Logic)
│   │   ├── fhir_search.py           # Document search
│   │   ├── kg_search.py             # Knowledge graph search
│   │   └── hybrid_search.py         # Multi-modal fusion
│   ├── vectorization/               # Document vectorization
│   └── validation/                  # Data validation & Health checks
├── config/                          # Configuration files
│   └── fhir_graphrag_config.aws.yaml  # Active AWS config
├── docs/                            # Documentation
│   ├── architecture.md              # System architecture
│   ├── deployment-guide.md          # AWS deployment
│   └── troubleshooting.md           # Common issues
├── scripts/                         # Deployment and utility scripts
│   └── aws/                         # AWS-specific scripts
├── tests/                           # Test suite
└── archive/                         # Historical implementations and docs

# Run backup (rsync to OneDrive folder)
./scripts/backup-to-onedrive.sh

# Unit tests
pytest tests/unit/

# Integration tests
pytest tests/integration/

# E2E tests
pytest tests/e2e/

import logging
logging.basicConfig(level=logging.DEBUG)

-- Future: Auto-computed embeddings on INSERT/UPDATE
CREATE TABLE ClinicalNoteVectors (
    ID INT PRIMARY KEY,
    TextContent TEXT,
    Embedding EMBEDDING[MODEL='NV-EmbedQA-E5-v5'](TextContent)  -- Auto-computed
);