# Architecture Overview

This document provides a comprehensive overview of Local Deep Research's system architecture.

## Table of Contents

- [System Components](#system-components)
- [Entry Points](#entry-points)
- [Research Execution Flow](#research-execution-flow)
  - [Research Status Lifecycle](#research-status-lifecycle)
- [Module Responsibilities](#module-responsibilities)
- [Threading Model](#threading-model)
- [Configuration System](#configuration-system)
- [Key Interfaces](#key-interfaces)

---

## System Components

```mermaid
graph TB
    subgraph "Entry Points"
        CLI[ldr CLI]
        WEB[ldr-web Flask App]
        API[REST API /api/v1]
    end

    subgraph "Core Research Engine"
        SS[SearchSystem<br/>search_system.py]
        SSF[StrategyFactory<br/>search_system_factory.py]
        RG[ReportGenerator<br/>report_generator.py]
    end

    subgraph "Search Layer"
        STRAT[32 Search Strategies<br/>advanced_search_system/strategies/]
        ENG[30+ Search Engines<br/>web_search_engines/engines/]
        RL[Rate Limiter<br/>rate_limiting/]
    end

    subgraph "Data Layer"
        DB[(SQLCipher DB<br/>Per-User Encrypted)]
        MODELS[20+ ORM Models<br/>database/models/]
        CACHE[Memory Cache]
    end

    subgraph "LLM Layer"
        PROV[LLM Providers<br/>Ollama, OpenAI, etc.]
        EMB[Embeddings<br/>embeddings/]
        RERANK[Reranker<br/>reranker/]
    end

    CLI --> SS
    WEB --> SS
    API --> SS

    SS --> SSF
    SS --> RG
    SSF --> STRAT
    STRAT --> ENG
    ENG --> RL

    SS --> PROV
    SS --> DB
    MODELS --> DB

    RG --> PROV
    ENG --> CACHE
```

---

## Entry Points

### Web Application (`ldr-web`)

**Location:** `src/local_deep_research/web/app.py`

The primary user interface. Launches a Flask server with SocketIO for real-time updates.

```mermaid
graph LR
    A[Browser] -->|HTTP/WS| B[Flask App]
    B --> C[Blueprints]
    C --> D[research_routes]
    C --> E[api_routes]
    C --> F[settings_routes]
    C --> G[auth_routes]
    B -->|Real-time| H[SocketIO]
```

**Key files:**
- `web/app.py` - Main entry, starts server
- `web/app_factory.py` - Flask app creation with middleware
- `web/routes/` - Blueprint route handlers
- `web/services/` - Business logic services

### REST API (`/api/v1`)

**Location:** `src/local_deep_research/web/api.py`

Programmatic access for integrations.

| Endpoint | Method | Purpose |
|----------|--------|---------|
| `/api/v1/quick_summary` | POST | Quick research summary |
| `/api/v1/generate_report` | POST | Full research report |
| `/api/v1/analyze_documents` | POST | Search local collections |
| `/api/v1/health` | GET | Health check |

---

## Research Execution Flow

```mermaid
sequenceDiagram
    participant User
    participant Web as Flask App
    participant SS as SearchSystem
    participant SF as StrategyFactory
    participant Strat as Strategy
    participant Eng as SearchEngine
    participant LLM as LLM Provider
    participant DB as Database

    User->>Web: Submit Query
    Web->>SS: start_research()
    SS->>SF: create_strategy(name)
    SF-->>SS: Strategy instance

    loop Research Iterations
        SS->>Strat: analyze_topic(query)
        Strat->>LLM: Generate questions
        LLM-->>Strat: Questions

        loop Per Question
            Strat->>Eng: search(question)
            Eng-->>Strat: Results
        end

        Strat->>LLM: Synthesize findings
        LLM-->>Strat: Synthesis
        Strat-->>SS: Findings
    end

    SS->>DB: Save results
    SS-->>Web: Research complete
    Web-->>User: Results via SocketIO
```

### Research Status Lifecycle

```mermaid
stateDiagram-v2
    [*] --> QUEUED : Concurrency limit reached
    [*] --> IN_PROGRESS : Slots available

    QUEUED --> IN_PROGRESS : Worker picks up task
    QUEUED --> SUSPENDED : User terminates

    IN_PROGRESS --> COMPLETED : Research succeeds
    IN_PROGRESS --> FAILED : Unrecoverable error
    IN_PROGRESS --> SUSPENDED : User terminates

    COMPLETED --> [*]
    FAILED --> [*]
    SUSPENDED --> [*]

    note right of FAILED
        Set by processor_v2 and
        research_service on errors
    end note

    note left of SUSPENDED
        Set when user clicks
        terminate/stop
    end note
```

> **Unused statuses:** `PENDING` (declared as a model default but never set by any creation
> path), `ERROR` (never set; predates `FAILED`), and `CANCELLED` (unused by research; used
> by benchmarks) exist in `ResearchStatus` for backward compatibility.

---

## Module Responsibilities

### Core Modules

| Module | Location | Responsibility |
|--------|----------|----------------|
| **SearchSystem** | `search_system.py` | Orchestrates research, coordinates strategies and engines |
| **StrategyFactory** | `search_system_factory.py` | Creates strategy instances based on configuration |
| **ReportGenerator** | `report_generator.py` | Generates structured reports from research findings |
| **CitationHandler** | `citation_handler.py` | Processes and validates citations |

### Search System

| Module | Location | Responsibility |
|--------|----------|----------------|
| **BaseSearchEngine** | `web_search_engines/search_engine_base.py` | Abstract base for all search engines |
| **SearchEngineFactory** | `web_search_engines/search_engine_factory.py` | Creates engine instances |
| **RateLimitTracker** | `web_search_engines/rate_limiting/tracker.py` | Adaptive rate limiting |
| **RetrieverRegistry** | `web_search_engines/retriever_registry.py` | LangChain retriever integration |

### Strategy System

| Module | Location | Responsibility |
|--------|----------|----------------|
| **BaseSearchStrategy** | `advanced_search_system/strategies/base_strategy.py` | Abstract base for strategies |
| **FindingsRepository** | `advanced_search_system/findings/` | Accumulates research findings |
| **QuestionGenerator** | `advanced_search_system/questions/` | Generates research questions |

### Web Application

| Module | Location | Responsibility |
|--------|----------|----------------|
| **SocketIOService** | `web/services/socket_service.py` | Real-time communication |
| **ResearchService** | `web/services/research_service.py` | Research execution |
| **QueueManager** | `web/queue/` | Background task queue |
| **SessionManager** | `web/auth/session_manager.py` | User session handling |

### Data Layer

| Module | Location | Responsibility |
|--------|----------|----------------|
| **Models** | `database/models/` | SQLAlchemy ORM models |
| **SessionContext** | `database/session_context.py` | Thread-safe DB sessions |
| **EncryptedDB** | `database/encrypted_db.py` | SQLCipher integration |

### LLM Integration

| Module | Location | Responsibility |
|--------|----------|----------------|
| **LLM Providers** | `llm/providers/implementations/` | Provider-specific LLM wrappers |
| **AutoDiscovery** | `llm/providers/auto_discovery.py` | Dynamic provider detection |
| **LLMRegistry** | `llm/llm_registry.py` | Custom LLM registration |

---

## Threading Model

```mermaid
graph TB
    subgraph "Main Thread"
        FLASK[Flask Server]
        SOCKETIO[SocketIO Handler]
    end

    subgraph "Research Threads"
        RT1[Research Thread 1]
        RT2[Research Thread 2]
        RTN[Research Thread N]
    end

    subgraph "Queue Processor"
        QP[Queue Processor Thread]
    end

    subgraph "Thread-Local Storage"
        TC[Thread Context<br/>Settings Snapshot]
        DBS[DB Session<br/>Per-User]
    end

    FLASK --> RT1
    FLASK --> RT2
    FLASK --> RTN

    RT1 --> TC
    RT2 --> TC
    RTN --> TC

    QP --> RT1

    RT1 -.-> SOCKETIO
    RT2 -.-> SOCKETIO
```

**Key Threading Concepts:**

1. **Thread Context** (`config/thread_settings.py`)
   - Each research thread has its own settings snapshot
   - Prevents race conditions on configuration changes

2. **Per-User DB Sessions** (`database/session_context.py`)
   - Each user has an isolated SQLCipher database
   - Sessions are thread-local via context manager

3. **Queue Processing** (`web/queue/`)
   - Background queue for long-running research
   - Processes items from `QueuedResearch` table

4. **SocketIO Updates**
   - Research threads emit progress via SocketIO
   - Uses threading async mode (not asyncio)

---

## Configuration System

```mermaid
graph TB
    subgraph "Configuration Sources"
        ENV[Environment Variables]
        DB[(Database Settings<br/>per-user)]
        JSON[Default Settings<br/>default_settings.json]
    end

    subgraph "Settings Management"
        SM[SettingsManager<br/>manager.py]
    end

    subgraph "Runtime Access"
        SNAP[Settings Snapshot<br/>Thread-safe copy]
        TC[Thread Context<br/>thread_settings.py]
    end

    ENV --> SM
    JSON --> SM
    DB --> SM
    SM --> SNAP
    SNAP --> TC
```

**Configuration Flow:**

1. **Defaults** - Default settings loaded from JSON
2. **Environment** - Environment variables override defaults
3. **Database** - User settings loaded from encrypted per-user DB
4. **Snapshot** - Thread-safe copy created for each research
5. **Access** - Code reads from snapshot via thread context

**Key Settings Categories:**

| Category | Examples |
|----------|----------|
| `llm.*` | Provider, model, temperature, API keys |
| `search.*` | Engine selection, max results, rate limits |
| `app.*` | Debug mode, logging, UI preferences |
| `notifications.*` | Email, webhook configurations |

---

## Key Interfaces

### Search Engine Interface

All search engines implement `BaseSearchEngine`:

```python
class BaseSearchEngine(ABC):
    # Classification flags
    is_public: bool = True
    is_generic: bool = True
    is_scientific: bool = False
    is_local: bool = False
    is_news: bool = False
    is_code: bool = False
    is_lexical: bool = False
    needs_llm_relevance_filter: bool = False

    @abstractmethod
    def run(self, query: str) -> List[Dict[str, Any]]:
        """Execute search and return results."""
        # Returns: [{"title": ..., "link": ..., "snippet": ...}]
```

### Strategy Interface

All strategies implement `BaseSearchStrategy`:

```python
class BaseSearchStrategy(ABC):
    def __init__(self, search, model, all_links_of_system,
                 settings_snapshot, **kwargs):
        ...

    @abstractmethod
    def analyze_topic(self, query: str) -> Dict:
        """Execute research strategy."""
        # Returns: {
        #     "findings": [...],
        #     "iterations": int,
        #     "questions": {...},
        #     "formatted_findings": str,
        #     "current_knowledge": {...}
        # }
```

### LLM Provider Interface

All providers extend `BaseLLMProvider` (most extend `OpenAICompatibleProvider`):

```python
class OpenAICompatibleProvider(BaseLLMProvider):
    provider_name: str
    api_key_setting: str | None      # Settings key, or None for no-key providers
    api_key_optional: bool = False   # If True, missing key uses placeholder
    url_setting: str
    default_base_url: str
    default_model: str

    @classmethod
    def create_llm(cls, model_name, temperature, **kwargs) -> BaseChatModel:
        """Create LangChain LLM instance."""
```

---

## Directory Structure

```
src/local_deep_research/
├── search_system.py           # Main orchestrator
├── search_system_factory.py   # Strategy factory
├── report_generator.py        # Report generation
├── citation_handler.py        # Citation processing
│
├── web/                       # Flask application
│   ├── app.py                # Entry point
│   ├── app_factory.py        # App creation
│   ├── routes/               # Blueprint handlers
│   ├── services/             # Business logic
│   ├── queue/                # Task queue
│   └── auth/                 # Authentication
│
├── advanced_search_system/    # Search strategies
│   ├── strategies/           # 32 strategy implementations
│   ├── questions/            # Question generation
│   ├── findings/             # Findings management
│   └── ...
│
├── web_search_engines/        # Search engines
│   ├── engines/              # 30+ engine implementations
│   ├── search_engine_base.py # Abstract base
│   ├── search_engine_factory.py
│   └── rate_limiting/        # Adaptive rate limiting
│
├── database/                  # Data layer
│   ├── models/               # 20+ ORM models
│   ├── session_context.py    # Session management
│   └── encrypted_db.py       # SQLCipher
│
├── llm/                       # LLM integration
│   ├── providers/            # Provider implementations
│   └── llm_registry.py       # Custom LLM registration
│
├── config/                    # Configuration
│   ├── llm_config.py         # LLM setup
│   ├── search_config.py      # Search setup
│   └── thread_settings.py    # Thread context
│
├── settings/                  # Settings management
│   └── manager.py            # SettingsManager
│
└── api/                       # Programmatic API
    ├── client.py             # HTTP client
    └── research_functions.py # Direct functions
```

---

## See Also

- [Database Schema](./DATABASE_SCHEMA.md) - Detailed data model documentation
- [Semantic Search](./SEMANTIC_SEARCH.md) - Indexing pipeline, search modes, and three-tier merge algorithm
- [Extension Guide](../developing/EXTENDING.md) - How to add custom components
- [Troubleshooting](../troubleshooting.md) - Common issues and solutions