Merge pull request #671 from ranfysvalle02/main

+ MongoDB KnowledgeGraph Support

examples/lightrag_openai_mongodb_graph_demo.py

@@ -0,0 +1,73 @@
+import os
+import asyncio
+from lightrag import LightRAG, QueryParam
+from lightrag.llm.openai import gpt_4o_mini_complete, openai_embed
+from lightrag.utils import EmbeddingFunc
+import numpy as np
+
+#########
+# Uncomment the below two lines if running in a jupyter notebook to handle the async nature of rag.insert()
+# import nest_asyncio
+# nest_asyncio.apply()
+#########
+WORKING_DIR = "./mongodb_test_dir"
+if not os.path.exists(WORKING_DIR):
+    os.mkdir(WORKING_DIR)
+
+
+os.environ["OPENAI_API_KEY"] = "sk-"
+os.environ["MONGO_URI"] = "mongodb://0.0.0.0:27017/?directConnection=true"
+os.environ["MONGO_DATABASE"] = "LightRAG"
+os.environ["MONGO_KG_COLLECTION"] = "MDB_KG"
+
+# Embedding Configuration and Functions
+EMBEDDING_MODEL = os.environ.get("EMBEDDING_MODEL", "text-embedding-3-large")
+EMBEDDING_MAX_TOKEN_SIZE = int(os.environ.get("EMBEDDING_MAX_TOKEN_SIZE", 8192))
+
+
+async def embedding_func(texts: list[str]) -> np.ndarray:
+    return await openai_embed(
+        texts,
+        model=EMBEDDING_MODEL,
+    )
+
+
+async def get_embedding_dimension():
+    test_text = ["This is a test sentence."]
+    embedding = await embedding_func(test_text)
+    return embedding.shape[1]
+
+
+async def create_embedding_function_instance():
+    # Get embedding dimension
+    embedding_dimension = await get_embedding_dimension()
+    # Create embedding function instance
+    return EmbeddingFunc(
+        embedding_dim=embedding_dimension,
+        max_token_size=EMBEDDING_MAX_TOKEN_SIZE,
+        func=embedding_func,
+    )
+
+
+async def initialize_rag():
+    embedding_func_instance = await create_embedding_function_instance()
+
+    return LightRAG(
+        working_dir=WORKING_DIR,
+        llm_model_func=gpt_4o_mini_complete,
+        embedding_func=embedding_func_instance,
+        graph_storage="MongoGraphStorage",
+        log_level="DEBUG",
+    )
+
+
+# Run the initialization
+rag = asyncio.run(initialize_rag())
+
+with open("book.txt", "r", encoding="utf-8") as f:
+    rag.insert(f.read())
+
+# Perform naive search
+print(
+    rag.query("What are the top themes in this story?", param=QueryParam(mode="naive"))
+)

lightrag/kg/mongo_impl.py

@@ -2,15 +2,18 @@ import os
 from tqdm.asyncio import tqdm as tqdm_async
 from dataclasses import dataclass
 import pipmaster as pm
+import np
 
 if not pm.is_installed("pymongo"):
     pm.install("pymongo")
 
 from pymongo import MongoClient
-from typing import Union
+from motor.motor_asyncio import AsyncIOMotorClient
+from typing import Union, List, Tuple
 from lightrag.utils import logger
 
 from lightrag.base import BaseKVStorage
+from lightrag.base import BaseGraphStorage
 
 
 @dataclass
@@ -78,3 +81,360 @@ class MongoKVStorage(BaseKVStorage):
     async def drop(self):
         """ """
         pass
+
+
+@dataclass
+class MongoGraphStorage(BaseGraphStorage):
+    """
+    A concrete implementation using MongoDB’s $graphLookup to demonstrate multi-hop queries.
+    """
+
+    def __init__(self, namespace, global_config, embedding_func):
+        super().__init__(
+            namespace=namespace,
+            global_config=global_config,
+            embedding_func=embedding_func,
+        )
+        self.client = AsyncIOMotorClient(
+            os.environ.get("MONGO_URI", "mongodb://root:root@localhost:27017/")
+        )
+        self.db = self.client[os.environ.get("MONGO_DATABASE", "LightRAG")]
+        self.collection = self.db[os.environ.get("MONGO_KG_COLLECTION", "MDB_KG")]
+
+    #
+    # -------------------------------------------------------------------------
+    # HELPER: $graphLookup pipeline
+    # -------------------------------------------------------------------------
+    #
+
+    async def _graph_lookup(
+        self, start_node_id: str, max_depth: int = None
+    ) -> List[dict]:
+        """
+        Performs a $graphLookup starting from 'start_node_id' and returns
+        all reachable documents (including the start node itself).
+
+        Pipeline Explanation:
+        - 1) $match: We match the start node document by _id = start_node_id.
+        - 2) $graphLookup:
+            "from": same collection,
+            "startWith": "$edges.target" (the immediate neighbors in 'edges'),
+            "connectFromField": "edges.target",
+            "connectToField": "_id",
+            "as": "reachableNodes",
+            "maxDepth": max_depth (if provided),
+            "depthField": "depth" (used for debugging or filtering).
+        - 3) We add an $project or $unwind as needed to extract data.
+        """
+        pipeline = [
+            {"$match": {"_id": start_node_id}},
+            {
+                "$graphLookup": {
+                    "from": self.collection.name,
+                    "startWith": "$edges.target",
+                    "connectFromField": "edges.target",
+                    "connectToField": "_id",
+                    "as": "reachableNodes",
+                    "depthField": "depth",
+                }
+            },
+        ]
+
+        # If you want a limited depth (e.g., only 1 or 2 hops), set maxDepth
+        if max_depth is not None:
+            pipeline[1]["$graphLookup"]["maxDepth"] = max_depth
+
+        # Return the matching doc plus a field "reachableNodes"
+        cursor = self.collection.aggregate(pipeline)
+        results = await cursor.to_list(None)
+
+        # If there's no matching node, results = [].
+        # Otherwise, results[0] is the start node doc,
+        # plus results[0]["reachableNodes"] is the array of connected docs.
+        return results
+
+    #
+    # -------------------------------------------------------------------------
+    # BASIC QUERIES
+    # -------------------------------------------------------------------------
+    #
+
+    async def has_node(self, node_id: str) -> bool:
+        """
+        Check if node_id is present in the collection by looking up its doc.
+        No real need for $graphLookup here, but let's keep it direct.
+        """
+        doc = await self.collection.find_one({"_id": node_id}, {"_id": 1})
+        return doc is not None
+
+    async def has_edge(self, source_node_id: str, target_node_id: str) -> bool:
+        """
+        Check if there's a direct single-hop edge from source_node_id to target_node_id.
+
+        We'll do a $graphLookup with maxDepth=0 from the source node—meaning
+        “Look up zero expansions.” Actually, for a direct edge check, we can do maxDepth=1
+        and then see if the target node is in the "reachableNodes" at depth=0.
+
+        But typically for a direct edge, we might just do a find_one.
+        Below is a demonstration approach.
+        """
+
+        # We can do a single-hop graphLookup (maxDepth=0 or 1).
+        # Then check if the target_node appears among the edges array.
+        pipeline = [
+            {"$match": {"_id": source_node_id}},
+            {
+                "$graphLookup": {
+                    "from": self.collection.name,
+                    "startWith": "$edges.target",
+                    "connectFromField": "edges.target",
+                    "connectToField": "_id",
+                    "as": "reachableNodes",
+                    "depthField": "depth",
+                    "maxDepth": 0,  # means: do not follow beyond immediate edges
+                }
+            },
+            {
+                "$project": {
+                    "_id": 0,
+                    "reachableNodes._id": 1,  # only keep the _id from the subdocs
+                }
+            },
+        ]
+        cursor = self.collection.aggregate(pipeline)
+        results = await cursor.to_list(None)
+        if not results:
+            return False
+
+        # results[0]["reachableNodes"] are the immediate neighbors
+        reachable_ids = [d["_id"] for d in results[0].get("reachableNodes", [])]
+        return target_node_id in reachable_ids
+
+    #
+    # -------------------------------------------------------------------------
+    # DEGREES
+    # -------------------------------------------------------------------------
+    #
+
+    async def node_degree(self, node_id: str) -> int:
+        """
+        Returns the total number of edges connected to node_id (both inbound and outbound).
+        The easiest approach is typically two queries:
+         - count of edges array in node_id's doc
+         - count of how many other docs have node_id in their edges.target.
+
+        But we'll do a $graphLookup demonstration for inbound edges:
+        1) Outbound edges: direct from node's edges array
+        2) Inbound edges: we can do a special $graphLookup from all docs
+           or do an explicit match.
+
+        For demonstration, let's do this in two steps (with second step $graphLookup).
+        """
+        # --- 1) Outbound edges (direct from doc) ---
+        doc = await self.collection.find_one({"_id": node_id}, {"edges": 1})
+        if not doc:
+            return 0
+        outbound_count = len(doc.get("edges", []))
+
+        # --- 2) Inbound edges:
+        # A simple way is: find all docs where "edges.target" == node_id.
+        # But let's do a $graphLookup from `node_id` in REVERSE.
+        # There's a trick to do "reverse" graphLookups: you'd store
+        # reversed edges or do a more advanced pipeline. Typically you'd do
+        # a direct match. We'll just do a direct match for inbound.
+        inbound_count_pipeline = [
+            {"$match": {"edges.target": node_id}},
+            {
+                "$project": {
+                    "matchingEdgesCount": {
+                        "$size": {
+                            "$filter": {
+                                "input": "$edges",
+                                "as": "edge",
+                                "cond": {"$eq": ["$$edge.target", node_id]},
+                            }
+                        }
+                    }
+                }
+            },
+            {"$group": {"_id": None, "totalInbound": {"$sum": "$matchingEdgesCount"}}},
+        ]
+        inbound_cursor = self.collection.aggregate(inbound_count_pipeline)
+        inbound_result = await inbound_cursor.to_list(None)
+        inbound_count = inbound_result[0]["totalInbound"] if inbound_result else 0
+
+        return outbound_count + inbound_count
+
+    async def edge_degree(self, src_id: str, tgt_id: str) -> int:
+        """
+        If your graph can hold multiple edges from the same src to the same tgt
+        (e.g. different 'relation' values), you can sum them. If it's always
+        one edge, this is typically 1 or 0.
+
+        We'll do a single-hop $graphLookup from src_id,
+        then count how many edges reference tgt_id at depth=0.
+        """
+        pipeline = [
+            {"$match": {"_id": src_id}},
+            {
+                "$graphLookup": {
+                    "from": self.collection.name,
+                    "startWith": "$edges.target",
+                    "connectFromField": "edges.target",
+                    "connectToField": "_id",
+                    "as": "neighbors",
+                    "depthField": "depth",
+                    "maxDepth": 0,
+                }
+            },
+            {"$project": {"edges": 1, "neighbors._id": 1, "neighbors.type": 1}},
+        ]
+        cursor = self.collection.aggregate(pipeline)
+        results = await cursor.to_list(None)
+        if not results:
+            return 0
+
+        # We can simply count how many edges in `results[0].edges` have target == tgt_id.
+        edges = results[0].get("edges", [])
+        count = sum(1 for e in edges if e.get("target") == tgt_id)
+        return count
+
+    #
+    # -------------------------------------------------------------------------
+    # GETTERS
+    # -------------------------------------------------------------------------
+    #
+
+    async def get_node(self, node_id: str) -> Union[dict, None]:
+        """
+        Return the full node document (including "edges"), or None if missing.
+        """
+        return await self.collection.find_one({"_id": node_id})
+
+    async def get_edge(
+        self, source_node_id: str, target_node_id: str
+    ) -> Union[dict, None]:
+        """
+        Return the first edge dict from source_node_id to target_node_id if it exists.
+        Uses a single-hop $graphLookup as demonstration, though a direct find is simpler.
+        """
+        pipeline = [
+            {"$match": {"_id": source_node_id}},
+            {
+                "$graphLookup": {
+                    "from": self.collection.name,
+                    "startWith": "$edges.target",
+                    "connectFromField": "edges.target",
+                    "connectToField": "_id",
+                    "as": "neighbors",
+                    "depthField": "depth",
+                    "maxDepth": 0,
+                }
+            },
+            {"$project": {"edges": 1}},
+        ]
+        cursor = self.collection.aggregate(pipeline)
+        docs = await cursor.to_list(None)
+        if not docs:
+            return None
+
+        for e in docs[0].get("edges", []):
+            if e.get("target") == target_node_id:
+                return e
+        return None
+
+    async def get_node_edges(
+        self, source_node_id: str
+    ) -> Union[List[Tuple[str, str]], None]:
+        """
+        Return a list of (target_id, relation) for direct edges from source_node_id.
+        Demonstrates $graphLookup at maxDepth=0, though direct doc retrieval is simpler.
+        """
+        pipeline = [
+            {"$match": {"_id": source_node_id}},
+            {
+                "$graphLookup": {
+                    "from": self.collection.name,
+                    "startWith": "$edges.target",
+                    "connectFromField": "edges.target",
+                    "connectToField": "_id",
+                    "as": "neighbors",
+                    "depthField": "depth",
+                    "maxDepth": 0,
+                }
+            },
+            {"$project": {"_id": 0, "edges": 1}},
+        ]
+        cursor = self.collection.aggregate(pipeline)
+        result = await cursor.to_list(None)
+        if not result:
+            return None
+
+        edges = result[0].get("edges", [])
+        return [(e["target"], e["relation"]) for e in edges]
+
+    #
+    # -------------------------------------------------------------------------
+    # UPSERTS
+    # -------------------------------------------------------------------------
+    #
+
+    async def upsert_node(self, node_id: str, node_data: dict):
+        """
+        Insert or update a node document. If new, create an empty edges array.
+        """
+        # By default, preserve existing 'edges'.
+        # We'll only set 'edges' to [] on insert (no overwrite).
+        update_doc = {"$set": {**node_data}, "$setOnInsert": {"edges": []}}
+        await self.collection.update_one({"_id": node_id}, update_doc, upsert=True)
+
+    async def upsert_edge(
+        self, source_node_id: str, target_node_id: str, edge_data: dict
+    ):
+        """
+        Upsert an edge from source_node_id -> target_node_id with optional 'relation'.
+        If an edge with the same target exists, we remove it and re-insert with updated data.
+        """
+        # Ensure source node exists
+        await self.upsert_node(source_node_id, {})
+
+        # Remove existing edge (if any)
+        await self.collection.update_one(
+            {"_id": source_node_id}, {"$pull": {"edges": {"target": target_node_id}}}
+        )
+
+        # Insert new edge
+        new_edge = {"target": target_node_id}
+        new_edge.update(edge_data)
+        await self.collection.update_one(
+            {"_id": source_node_id}, {"$push": {"edges": new_edge}}
+        )
+
+    #
+    # -------------------------------------------------------------------------
+    # DELETION
+    # -------------------------------------------------------------------------
+    #
+
+    async def delete_node(self, node_id: str):
+        """
+        1) Remove node’s doc entirely.
+        2) Remove inbound edges from any doc that references node_id.
+        """
+        # Remove inbound edges from all other docs
+        await self.collection.update_many({}, {"$pull": {"edges": {"target": node_id}}})
+
+        # Remove the node doc
+        await self.collection.delete_one({"_id": node_id})
+
+    #
+    # -------------------------------------------------------------------------
+    # EMBEDDINGS (NOT IMPLEMENTED)
+    # -------------------------------------------------------------------------
+    #
+
+    async def embed_nodes(self, algorithm: str) -> Tuple[np.ndarray, List[str]]:
+        """
+        Placeholder for demonstration, raises NotImplementedError.
+        """
+        raise NotImplementedError("Node embedding is not used in lightrag.")

lightrag/lightrag.py

@@ -48,6 +48,7 @@ STORAGES = {
     "OracleVectorDBStorage": ".kg.oracle_impl",
     "MilvusVectorDBStorge": ".kg.milvus_impl",
     "MongoKVStorage": ".kg.mongo_impl",
+    "MongoGraphStorage": ".kg.mongo_impl",
     "RedisKVStorage": ".kg.redis_impl",
     "ChromaVectorDBStorage": ".kg.chroma_impl",
     "TiDBKVStorage": ".kg.tidb_impl",