Initial commit: RAG MCP Server with relationship graph

Features:
- Vector search with Pinecone + Vertex AI embeddings
- Document relationships (link, unlink, related, graph)
- Auto-link with LLM analysis
- Intelligent merge with Gemini

Modular structure:
- clients/: Pinecone, Vertex AI
- tools/: core, relations, stats
- utils/: validation, logging

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

utils/__init__.py

@@ -0,0 +1,11 @@
+"""Utility modules for RAG system."""
+from .validation import validate_content, validate_tag, validate_document_id
+from .logging import setup_logging, get_logger
+
+__all__ = [
+    "validate_content",
+    "validate_tag",
+    "validate_document_id",
+    "setup_logging",
+    "get_logger"
+]

utils/logging.py

@@ -0,0 +1,30 @@
+"""Logging configuration for RAG system."""
+import logging
+import sys
+
+def setup_logging(level: str = "INFO") -> None:
+    """
+    Setup logging configuration.
+
+    Args:
+        level: Logging level (DEBUG, INFO, WARNING, ERROR, CRITICAL)
+    """
+    logging.basicConfig(
+        level=getattr(logging, level.upper(), logging.INFO),
+        format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
+        handlers=[
+            logging.StreamHandler(sys.stdout)
+        ]
+    )
+
+def get_logger(name: str) -> logging.Logger:
+    """
+    Get logger instance.
+
+    Args:
+        name: Logger name (usually __name__)
+
+    Returns:
+        Logger instance
+    """
+    return logging.getLogger(name)

utils/validation.py

@@ -0,0 +1,91 @@
+"""Input validation functions for RAG system."""
+from config import MAX_CONTENT_LENGTH, MAX_TAG_LENGTH
+import re
+
+def validate_content(content: str) -> tuple[bool, str]:
+    """
+    Validate content string.
+
+    Args:
+        content: Content to validate
+
+    Returns:
+        (is_valid, error_message)
+    """
+    if not content or not content.strip():
+        return False, "Content cannot be empty"
+
+    if len(content) > MAX_CONTENT_LENGTH:
+        return False, f"Content exceeds maximum length of {MAX_CONTENT_LENGTH} characters"
+
+    return True, ""
+
+def validate_tag(tag: str) -> tuple[bool, str]:
+    """
+    Validate tag string.
+
+    Args:
+        tag: Tag to validate
+
+    Returns:
+        (is_valid, error_message)
+    """
+    if not tag or not tag.strip():
+        return False, "Tag cannot be empty"
+
+    if len(tag) > MAX_TAG_LENGTH:
+        return False, f"Tag exceeds maximum length of {MAX_TAG_LENGTH} characters"
+
+    # Only allow alphanumeric, underscore, hyphen
+    if not re.match(r'^[a-zA-Z0-9_-]+$', tag):
+        return False, "Tag must contain only alphanumeric characters, underscores, and hyphens"
+
+    return True, ""
+
+def validate_document_id(doc_id: str) -> tuple[bool, str]:
+    """
+    Validate document ID format.
+
+    Args:
+        doc_id: Document ID to validate
+
+    Returns:
+        (is_valid, error_message)
+    """
+    if not doc_id or not doc_id.strip():
+        return False, "Document ID cannot be empty"
+
+    # Basic UUID format check (flexible for various ID formats)
+    if len(doc_id) < 8 or len(doc_id) > 100:
+        return False, "Document ID must be between 8 and 100 characters"
+
+    return True, ""
+
+def sanitize_for_prompt(text: str) -> str:
+    """
+    Sanitize text to prevent prompt injection attacks.
+
+    Args:
+        text: Text to sanitize
+
+    Returns:
+        Sanitized text
+    """
+    # Remove common prompt injection patterns
+    dangerous_patterns = [
+        r'(?i)ignore\s+previous\s+instructions',
+        r'(?i)ignore\s+all\s+previous',
+        r'(?i)disregard\s+previous',
+        r'(?i)you\s+are\s+now',
+        r'(?i)system\s+prompt',
+        r'(?i)bypass\s+filters',
+    ]
+
+    sanitized = text
+    for pattern in dangerous_patterns:
+        sanitized = re.sub(pattern, '[FILTERED]', sanitized)
+
+    # Limit repeated characters
+    sanitized = re.sub(r'(.)\1{20,}', r'\1' * 20, sanitized)
+
+    return sanitized