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>
This commit is contained in:
kappa
2026-02-03 11:05:45 +09:00
commit 2858e0a344
17 changed files with 1450 additions and 0 deletions

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tools/__init__.py Normal file
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"""MCP tools for RAG operations."""
from .core import rag_save, rag_retrieve, rag_update, rag_delete
from .relations import rag_link, rag_unlink, rag_related, rag_graph
from .stats import rag_stats
__all__ = [
"rag_save",
"rag_retrieve",
"rag_update",
"rag_delete",
"rag_link",
"rag_unlink",
"rag_related",
"rag_graph",
"rag_stats"
]

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tools/core.py Normal file
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"""Core RAG tools: save, retrieve, update, delete."""
import uuid
from typing import Optional
from clients import get_index, get_embedding, merge_with_llm, analyze_relations_with_llm
from utils.logging import get_logger
from utils.validation import validate_content, validate_tag, validate_document_id
from config import AUTO_LINK_THRESHOLD, AUTO_LINK_TOP_K
from .relations import (
parse_relation,
format_relation,
_add_reverse_relation,
_remove_reverse_relation
)
import time
import threading
logger = get_logger(__name__)
# Rate limiting (in-memory counter)
_rate_limiter = {
"requests": [],
"lock": threading.Lock()
}
MAX_REQUESTS_PER_MINUTE = 60
def rate_limit_check() -> bool:
"""
Check if rate limit is exceeded.
Returns:
True if allowed, False if rate limit exceeded
"""
with _rate_limiter["lock"]:
now = time.time()
# Remove requests older than 1 minute
_rate_limiter["requests"] = [
req_time for req_time in _rate_limiter["requests"]
if now - req_time < 60
]
if len(_rate_limiter["requests"]) >= MAX_REQUESTS_PER_MINUTE:
return False
_rate_limiter["requests"].append(now)
return True
def rag_save(content: str, tag: Optional[str] = "general", relations: Optional[str] = None, auto_link: bool = False) -> str:
"""
Save important information to vector database.
Args:
content: Text content to save
tag: Tag for filtering (default: general)
relations: Comma-separated relations (e.g., "id1:depends_on,id2:see_also")
auto_link: Auto-create relations using LLM analysis
Returns:
Success message with document ID or error message
"""
if not rate_limit_check():
logger.warning("Rate limit exceeded for rag_save")
return "Error: Rate limit exceeded. Please wait before retrying."
# Validate inputs
is_valid, error_msg = validate_content(content)
if not is_valid:
logger.warning(f"Content validation failed: {error_msg}")
return f"Error: {error_msg}"
is_valid, error_msg = validate_tag(tag)
if not is_valid:
logger.warning(f"Tag validation failed: {error_msg}")
return f"Error: {error_msg}"
try:
index = get_index()
vector = get_embedding(content)
doc_id = str(uuid.uuid4())
# Parse manual relations
rel_list = []
if relations:
rel_list = [r.strip() for r in relations.split(',') if r.strip()]
# Auto-create relations
auto_relations = []
if auto_link:
logger.info(f"Auto-linking document with threshold={AUTO_LINK_THRESHOLD}, top_k={AUTO_LINK_TOP_K}")
# Search similar documents
similar_results = index.query(
vector=vector,
top_k=AUTO_LINK_TOP_K,
include_metadata=True
)
# Filter by threshold
similar_docs = []
for match in similar_results.get("matches", []):
if match.get("score", 0) >= AUTO_LINK_THRESHOLD:
similar_docs.append({
"id": match["id"],
"text": match["metadata"].get("text", ""),
"tag": match["metadata"].get("tag", ""),
"score": match["score"]
})
# LLM relation analysis
if similar_docs:
analyzed = analyze_relations_with_llm(content, tag, similar_docs)
for rel in analyzed:
rel_str = format_relation(rel["id"], rel["relation"])
if rel_str not in rel_list:
rel_list.append(rel_str)
auto_relations.append(rel_str)
metadata = {
"text": content,
"tag": tag,
"relations": rel_list
}
index.upsert(vectors=[{
"id": doc_id,
"values": vector,
"metadata": metadata
}])
# Create bidirectional relations
for rel_str in rel_list:
target_id, rel_type = parse_relation(rel_str)
_add_reverse_relation(target_id, doc_id, rel_type)
# Format result
result = f"Saved with ID: {doc_id}"
if auto_relations:
result += f"\n\nAuto-linked ({len(auto_relations)}):"
for rel in auto_relations:
target_id, rel_type = parse_relation(rel)
result += f"\n --[{rel_type}]--> {target_id[:8]}..."
if relations:
result += f"\nManual relations: {relations}"
logger.info(f"Document saved: {doc_id}, tag={tag}, relations={len(rel_list)}")
return result
except Exception as e:
logger.error(f"rag_save failed: {str(e)}", exc_info=True)
return f"Error: {str(e)}"
def rag_retrieve(query: str, top_k: int = 3, tag: Optional[str] = None) -> str:
"""
Retrieve relevant information from vector database.
Args:
query: Search query
top_k: Number of results to return (default: 3)
tag: Filter by specific tag (default: None, search all)
Returns:
Formatted search results or error message
"""
if not rate_limit_check():
logger.warning("Rate limit exceeded for rag_retrieve")
return "Error: Rate limit exceeded. Please wait before retrying."
# Validate query
is_valid, error_msg = validate_content(query)
if not is_valid:
logger.warning(f"Query validation failed: {error_msg}")
return f"Error: {error_msg}"
try:
index = get_index()
query_vector = get_embedding(query)
filter_dict = {"tag": {"$eq": tag}} if tag else None
results = index.query(
vector=query_vector,
top_k=top_k,
include_metadata=True,
filter=filter_dict
)
if not results["matches"]:
logger.info("No matching documents found")
return "관련된 정보를 찾지 못했습니다."
formatted = []
for i, res in enumerate(results["matches"], 1):
if "metadata" in res:
text = res["metadata"]["text"]
tag_val = res["metadata"].get("tag", "")
relations = res["metadata"].get("relations", [])
doc_id = res["id"]
score = res.get("score", 0)
entry = f"[{i}] ID: {doc_id} (score: {score:.3f}, tag: {tag_val})"
if relations:
entry += f"\n Relations: {relations}"
entry += f"\n {text}"
formatted.append(entry)
logger.info(f"Retrieved {len(formatted)} documents for query")
return "검색 결과:\n" + "\n---\n".join(formatted)
except Exception as e:
logger.error(f"rag_retrieve failed: {str(e)}", exc_info=True)
return f"Error: {str(e)}"
def rag_update(id: str, new_info: str) -> str:
"""
Intelligently merge existing and new information.
Args:
id: Document ID to update
new_info: New information to add or merge
Returns:
Update summary or error message
"""
if not rate_limit_check():
logger.warning("Rate limit exceeded for rag_update")
return "Error: Rate limit exceeded. Please wait before retrying."
# Validate inputs
is_valid, error_msg = validate_document_id(id)
if not is_valid:
logger.warning(f"Document ID validation failed: {error_msg}")
return f"Error: {error_msg}"
is_valid, error_msg = validate_content(new_info)
if not is_valid:
logger.warning(f"New info validation failed: {error_msg}")
return f"Error: {error_msg}"
try:
index = get_index()
result = index.fetch(ids=[id])
if id not in result["vectors"]:
logger.warning(f"Document not found: {id}")
return f"Error: Not found: {id}"
old_metadata = result["vectors"][id]["metadata"]
old_text = old_metadata.get("text", "")
tag = old_metadata.get("tag", "general")
relations = old_metadata.get("relations", [])
merged = merge_with_llm(old_text, new_info)
vector = get_embedding(merged)
index.upsert(vectors=[{
"id": id,
"values": vector,
"metadata": {"text": merged, "tag": tag, "relations": relations}
}])
logger.info(f"Document updated: {id}")
return f"Updated: {id}\n\n[기존]\n{old_text}\n\n[새 정보]\n{new_info}\n\n[병합 결과]\n{merged}"
except Exception as e:
logger.error(f"rag_update failed: {str(e)}", exc_info=True)
return f"Error: {str(e)}"
def rag_delete(id: str) -> str:
"""
Delete document by ID.
Args:
id: Document ID to delete
Returns:
Success message or error message
"""
if not rate_limit_check():
logger.warning("Rate limit exceeded for rag_delete")
return "Error: Rate limit exceeded. Please wait before retrying."
# Validate input
is_valid, error_msg = validate_document_id(id)
if not is_valid:
logger.warning(f"Document ID validation failed: {error_msg}")
return f"Error: {error_msg}"
try:
index = get_index()
# Remove reverse relations
result = index.fetch(ids=[id])
if id in result["vectors"]:
relations = result["vectors"][id]["metadata"].get("relations", [])
for rel_str in relations:
target_id, _ = parse_relation(rel_str)
_remove_reverse_relation(target_id, id)
index.delete(ids=[id])
logger.info(f"Document deleted: {id}")
return f"Deleted: {id}"
except Exception as e:
logger.error(f"rag_delete failed: {str(e)}", exc_info=True)
return f"Error: {str(e)}"

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"""Relation management tools and utilities."""
from typing import Optional
from collections import deque
from clients import get_index
from utils.logging import get_logger
from utils.validation import validate_document_id
from config import MAX_GRAPH_NODES
logger = get_logger(__name__)
# ============================================================
# Relation utility functions
# ============================================================
def parse_relation(rel_str: str) -> tuple:
"""
Parse 'id:type' format to (id, type).
Args:
rel_str: Relation string in format "id:type"
Returns:
(id, type) tuple
"""
if ':' in rel_str:
parts = rel_str.split(':', 1)
return (parts[0], parts[1])
return (rel_str, 'related')
def format_relation(doc_id: str, rel_type: str) -> str:
"""
Format (id, type) to 'id:type' string.
Args:
doc_id: Document ID
rel_type: Relation type
Returns:
Formatted relation string
"""
return f"{doc_id}:{rel_type}"
def get_reverse_relation(rel_type: str) -> str:
"""
Get reverse relation type.
Args:
rel_type: Relation type
Returns:
Reverse relation type
"""
reverse_map = {
'depends_on': 'required_by',
'required_by': 'depends_on',
'part_of': 'contains',
'contains': 'part_of',
'see_also': 'see_also',
'related': 'related',
'blocks': 'blocked_by',
'blocked_by': 'blocks',
'extends': 'extended_by',
'extended_by': 'extends',
'updates': 'updated_by',
'updated_by': 'updates',
}
return reverse_map.get(rel_type, f"reverse_{rel_type}")
def _add_reverse_relation(target_id: str, source_id: str, rel_type: str) -> bool:
"""
Internal: Add reverse relation to target document.
Args:
target_id: Target document ID
source_id: Source document ID
rel_type: Relation type (forward)
Returns:
True if successful, False otherwise
"""
try:
index = get_index()
result = index.fetch(ids=[target_id])
if target_id not in result["vectors"]:
logger.warning(f"Target document not found for reverse relation: {target_id}")
return False
metadata = result["vectors"][target_id]["metadata"]
relations = metadata.get("relations", [])
reverse_rel = format_relation(source_id, get_reverse_relation(rel_type))
if reverse_rel not in relations:
relations.append(reverse_rel)
metadata["relations"] = relations
vector = result["vectors"][target_id]["values"]
index.upsert(vectors=[{
"id": target_id,
"values": vector,
"metadata": metadata
}])
logger.debug(f"Added reverse relation: {target_id} <- {source_id}")
return True
return True
except Exception as e:
logger.error(f"Failed to add reverse relation: {str(e)}")
return False
def _remove_reverse_relation(target_id: str, source_id: str) -> bool:
"""
Internal: Remove reverse relation from target document.
Args:
target_id: Target document ID
source_id: Source document ID
Returns:
True if successful, False otherwise
"""
try:
index = get_index()
result = index.fetch(ids=[target_id])
if target_id not in result["vectors"]:
logger.warning(f"Target document not found for reverse relation removal: {target_id}")
return False
metadata = result["vectors"][target_id]["metadata"]
relations = metadata.get("relations", [])
relations = [r for r in relations if not r.startswith(f"{source_id}:")]
metadata["relations"] = relations
vector = result["vectors"][target_id]["values"]
index.upsert(vectors=[{
"id": target_id,
"values": vector,
"metadata": metadata
}])
logger.debug(f"Removed reverse relation: {target_id} <- {source_id}")
return True
except Exception as e:
logger.error(f"Failed to remove reverse relation: {str(e)}")
return False
# ============================================================
# MCP Tools
# ============================================================
def rag_link(from_id: str, to_id: str, relation_type: str = "related") -> str:
"""
Create relation between two documents (bidirectional).
Args:
from_id: Source document ID
to_id: Target document ID
relation_type: Relation type (depends_on, part_of, see_also, blocks, extends, updates, related)
Returns:
Success message or error message
"""
# Validate inputs
is_valid, error_msg = validate_document_id(from_id)
if not is_valid:
logger.warning(f"Source ID validation failed: {error_msg}")
return f"Error: {error_msg}"
is_valid, error_msg = validate_document_id(to_id)
if not is_valid:
logger.warning(f"Target ID validation failed: {error_msg}")
return f"Error: {error_msg}"
try:
index = get_index()
result = index.fetch(ids=[from_id])
if from_id not in result["vectors"]:
logger.warning(f"Source document not found: {from_id}")
return f"Error: Source document not found: {from_id}"
from_metadata = result["vectors"][from_id]["metadata"]
from_relations = from_metadata.get("relations", [])
new_rel = format_relation(to_id, relation_type)
if new_rel in from_relations:
logger.info(f"Relation already exists: {from_id} -> {to_id}")
return f"Relation already exists: {from_id} --[{relation_type}]--> {to_id}"
from_relations.append(new_rel)
from_metadata["relations"] = from_relations
from_vector = result["vectors"][from_id]["values"]
index.upsert(vectors=[{
"id": from_id,
"values": from_vector,
"metadata": from_metadata
}])
_add_reverse_relation(to_id, from_id, relation_type)
reverse_type = get_reverse_relation(relation_type)
logger.info(f"Linked: {from_id} --[{relation_type}]--> {to_id}")
return f"Linked: {from_id} --[{relation_type}]--> {to_id}\nReverse: {to_id} --[{reverse_type}]--> {from_id}"
except Exception as e:
logger.error(f"rag_link failed: {str(e)}", exc_info=True)
return f"Error: {str(e)}"
def rag_unlink(from_id: str, to_id: str) -> str:
"""
Remove relation between two documents (bidirectional).
Args:
from_id: Source document ID
to_id: Target document ID
Returns:
Success message or error message
"""
# Validate inputs
is_valid, error_msg = validate_document_id(from_id)
if not is_valid:
logger.warning(f"Source ID validation failed: {error_msg}")
return f"Error: {error_msg}"
is_valid, error_msg = validate_document_id(to_id)
if not is_valid:
logger.warning(f"Target ID validation failed: {error_msg}")
return f"Error: {error_msg}"
try:
index = get_index()
result = index.fetch(ids=[from_id])
if from_id not in result["vectors"]:
logger.warning(f"Document not found: {from_id}")
return f"Error: Document not found: {from_id}"
from_metadata = result["vectors"][from_id]["metadata"]
from_relations = from_metadata.get("relations", [])
original_count = len(from_relations)
from_relations = [r for r in from_relations if not r.startswith(f"{to_id}:")]
if len(from_relations) == original_count:
logger.info(f"No relation found: {from_id} -> {to_id}")
return f"No relation found from {from_id} to {to_id}"
from_metadata["relations"] = from_relations
from_vector = result["vectors"][from_id]["values"]
index.upsert(vectors=[{
"id": from_id,
"values": from_vector,
"metadata": from_metadata
}])
_remove_reverse_relation(to_id, from_id)
logger.info(f"Unlinked: {from_id} <--> {to_id}")
return f"Unlinked: {from_id} <--> {to_id}"
except Exception as e:
logger.error(f"rag_unlink failed: {str(e)}", exc_info=True)
return f"Error: {str(e)}"
def rag_related(id: str, relation_type: Optional[str] = None, include_content: bool = False) -> str:
"""
Query related documents.
Args:
id: Document ID to query
relation_type: Filter by specific relation type (default: all)
include_content: Include document content (default: False)
Returns:
Formatted relation list or error message
"""
# Validate input
is_valid, error_msg = validate_document_id(id)
if not is_valid:
logger.warning(f"Document ID validation failed: {error_msg}")
return f"Error: {error_msg}"
try:
index = get_index()
result = index.fetch(ids=[id])
if id not in result["vectors"]:
logger.warning(f"Document not found: {id}")
return f"Error: Document not found: {id}"
metadata = result["vectors"][id]["metadata"]
relations = metadata.get("relations", [])
if not relations:
logger.info(f"No relations found for: {id}")
return f"No relations found for: {id}"
if relation_type:
relations = [r for r in relations if r.endswith(f":{relation_type}")]
if not relations:
logger.info(f"No '{relation_type}' relations found for: {id}")
return f"No '{relation_type}' relations found for: {id}"
output = [f"Relations for {id}:"]
if include_content:
related_ids = [parse_relation(r)[0] for r in relations]
related_docs = index.fetch(ids=related_ids)
for rel_str in relations:
target_id, rel_type = parse_relation(rel_str)
entry = f"\n --[{rel_type}]--> {target_id}"
if target_id in related_docs["vectors"]:
text = related_docs["vectors"][target_id]["metadata"].get("text", "")
tag = related_docs["vectors"][target_id]["metadata"].get("tag", "")
preview = text[:200] + "..." if len(text) > 200 else text
entry += f"\n Tag: {tag}"
entry += f"\n {preview}"
output.append(entry)
else:
for rel_str in relations:
target_id, rel_type = parse_relation(rel_str)
output.append(f" --[{rel_type}]--> {target_id}")
logger.info(f"Found {len(relations)} relations for: {id}")
return "\n".join(output)
except Exception as e:
logger.error(f"rag_related failed: {str(e)}", exc_info=True)
return f"Error: {str(e)}"
def rag_graph(id: str, depth: int = 1) -> str:
"""
Explore relation graph from a document using BFS.
Args:
id: Starting document ID
depth: Search depth (default: 1, max: 3)
Returns:
Formatted graph or error message
"""
# Validate input
is_valid, error_msg = validate_document_id(id)
if not is_valid:
logger.warning(f"Document ID validation failed: {error_msg}")
return f"Error: {error_msg}"
try:
index = get_index()
depth = min(depth, 3)
visited = set()
nodes = {}
edges = []
queue = deque([(id, 0)]) # BFS queue with (doc_id, current_depth)
while queue and len(visited) < MAX_GRAPH_NODES:
doc_id, current_depth = queue.popleft()
if doc_id in visited or current_depth > depth:
continue
visited.add(doc_id)
result = index.fetch(ids=[doc_id])
if doc_id not in result["vectors"]:
continue
metadata = result["vectors"][doc_id]["metadata"]
text = metadata.get("text", "")
tag = metadata.get("tag", "")
relations = metadata.get("relations", [])
nodes[doc_id] = {
"tag": tag,
"preview": text[:100] + "..." if len(text) > 100 else text,
"depth": current_depth
}
for rel_str in relations:
target_id, rel_type = parse_relation(rel_str)
edges.append({
"from": doc_id,
"to": target_id,
"type": rel_type
})
if target_id not in visited and len(visited) < MAX_GRAPH_NODES:
queue.append((target_id, current_depth + 1))
if not nodes:
logger.warning(f"Document not found: {id}")
return f"Error: Document not found: {id}"
output = [f"=== Graph from {id} (depth: {depth}) ==="]
if len(visited) >= MAX_GRAPH_NODES:
output.append(f"\n[WARNING] Graph limited to {MAX_GRAPH_NODES} nodes\n")
output.append("Nodes:")
for node_id, info in sorted(nodes.items(), key=lambda x: x[1]["depth"]):
indent = " " * info["depth"]
output.append(f"{indent}[{info['tag']}] {node_id}")
output.append(f"{indent} {info['preview']}")
output.append(f"\nEdges ({len(edges)}):")
for edge in edges:
output.append(f" {edge['from'][:8]}... --[{edge['type']}]--> {edge['to'][:8]}...")
logger.info(f"Graph traversed: {len(nodes)} nodes, {len(edges)} edges")
return "\n".join(output)
except Exception as e:
logger.error(f"rag_graph failed: {str(e)}", exc_info=True)
return f"Error: {str(e)}"

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"""Statistics and monitoring tools."""
from clients import get_index
from utils.logging import get_logger
from config import AUTO_LINK_THRESHOLD, AUTO_LINK_TOP_K
logger = get_logger(__name__)
def rag_stats() -> str:
"""
Return RAG database statistics.
Returns:
Formatted statistics or error message
"""
try:
index = get_index()
stats = index.describe_index_stats()
total = stats.get("total_vector_count", 0)
output = [
"=== RAG Statistics ===",
f"Total documents: {total}",
f"Dimension: {stats.get('dimension', 'N/A')}",
f"Index fullness: {stats.get('index_fullness', 'N/A')}",
"",
"=== Auto-link Settings ===",
f"Threshold: {AUTO_LINK_THRESHOLD}",
f"Top-K candidates: {AUTO_LINK_TOP_K}"
]
logger.info(f"Stats retrieved: {total} documents")
return "\n".join(output)
except Exception as e:
logger.error(f"rag_stats failed: {str(e)}", exc_info=True)
return f"Error: {str(e)}"