Add entity/relation chunk tracking with configurable source ID limits

- Add entity_chunks & relation_chunks storage
- Implement KEEP/FIFO limit strategies
- Update env.example with new settings
- Add migration for chunk tracking data
- Support all KV storage

env.example

@@ -73,8 +73,11 @@ ENABLE_LLM_CACHE=true
 # MAX_RELATION_TOKENS=8000
 ### control the maximum tokens send to LLM (include entities, relations and chunks)
 # MAX_TOTAL_TOKENS=30000
-### control the maximum chunk_ids stored
+### control the maximum chunk_ids stored in vector and graph db
-# MAX_SOURCE_IDS_PER_ENTITY=500
+# MAX_SOURCE_IDS_PER_ENTITY=300
+# MAX_SOURCE_IDS_PER_RELATION=300
+### control chunk_ids limitation method: KEEP, FIFO (KEPP: Ingore New Chunks, FIFO: New chunks replace old chunks)
+# SOURCE_IDS_LIMIT_METHOD=KEEP
 
 ### maximum number of related chunks per source entity or relation
 ###     The chunk picker uses this value to determine the total number of chunks selected from KG(knowledge graph)

lightrag/api/routers/document_routes.py

@@ -2003,6 +2003,8 @@ def create_document_routes(
                 rag.full_docs,
                 rag.full_entities,
                 rag.full_relations,
+                rag.entity_chunks,
+                rag.relation_chunks,
                 rag.entities_vdb,
                 rag.relationships_vdb,
                 rag.chunks_vdb,

lightrag/base.py

@@ -355,6 +355,14 @@ class BaseKVStorage(StorageNameSpace, ABC):
             None
         """
 
+    @abstractmethod
+    async def is_empty(self) -> bool:
+        """Check if the storage is empty
+
+        Returns:
+            bool: True if storage contains no data, False otherwise
+        """
+
 
 @dataclass
 class BaseGraphStorage(StorageNameSpace, ABC):

lightrag/constants.py

@@ -13,7 +13,16 @@ DEFAULT_MAX_GRAPH_NODES = 1000
 # Default values for extraction settings
 DEFAULT_SUMMARY_LANGUAGE = "English"  # Default language for document processing
 DEFAULT_MAX_GLEANING = 1
-DEFAULT_MAX_SOURCE_IDS_PER_ENTITY = 500 # Applies to Both Graph + Vector DBs
+
+DEFAULT_MAX_SOURCE_IDS_PER_ENTITY = 3
+DEFAULT_MAX_SOURCE_IDS_PER_RELATION = 3
+SOURCE_IDS_LIMIT_METHOD_KEEP = "KEEP"
+SOURCE_IDS_LIMIT_METHOD_FIFO = "FIFO"
+DEFAULT_SOURCE_IDS_LIMIT_METHOD = SOURCE_IDS_LIMIT_METHOD_KEEP
+VALID_SOURCE_IDS_LIMIT_METHODS = {
+    SOURCE_IDS_LIMIT_METHOD_KEEP,
+    SOURCE_IDS_LIMIT_METHOD_FIFO,
+}
 
 # Number of description fragments to trigger LLM summary
 DEFAULT_FORCE_LLM_SUMMARY_ON_MERGE = 8

lightrag/kg/json_doc_status_impl.py

@@ -187,6 +187,20 @@ class JsonDocStatusStorage(DocStatusStorage):
 
         await self.index_done_callback()
 
+    async def is_empty(self) -> bool:
+        """Check if the storage is empty
+
+        Returns:
+            bool: True if storage is empty, False otherwise
+
+        Raises:
+            StorageNotInitializedError: If storage is not initialized
+        """
+        if self._storage_lock is None:
+            raise StorageNotInitializedError("JsonDocStatusStorage")
+        async with self._storage_lock:
+            return len(self._data) == 0
+
     async def get_by_id(self, id: str) -> Union[dict[str, Any], None]:
         async with self._storage_lock:
             return self._data.get(id)

lightrag/kg/json_kv_impl.py

@@ -84,26 +84,6 @@ class JsonKVStorage(BaseKVStorage):
                 write_json(data_dict, self._file_name)
                 await clear_all_update_flags(self.final_namespace)
 
-    async def get_all(self) -> dict[str, Any]:
-        """Get all data from storage
-
-        Returns:
-            Dictionary containing all stored data
-        """
-        async with self._storage_lock:
-            result = {}
-            for key, value in self._data.items():
-                if value:
-                    # Create a copy to avoid modifying the original data
-                    data = dict(value)
-                    # Ensure time fields are present, provide default values for old data
-                    data.setdefault("create_time", 0)
-                    data.setdefault("update_time", 0)
-                    result[key] = data
-                else:
-                    result[key] = value
-            return result
-
     async def get_by_id(self, id: str) -> dict[str, Any] | None:
         async with self._storage_lock:
             result = self._data.get(id)
@@ -200,6 +180,15 @@ class JsonKVStorage(BaseKVStorage):
             if any_deleted:
                 await set_all_update_flags(self.final_namespace)
 
+    async def is_empty(self) -> bool:
+        """Check if the storage is empty
+
+        Returns:
+            bool: True if storage contains no data, False otherwise
+        """
+        async with self._storage_lock:
+            return len(self._data) == 0
+
     async def drop(self) -> dict[str, str]:
         """Drop all data from storage and clean up resources
            This action will persistent the data to disk immediately.

lightrag/kg/mongo_impl.py

@@ -175,22 +175,6 @@ class MongoKVStorage(BaseKVStorage):
         existing_ids = {str(x["_id"]) async for x in cursor}
         return keys - existing_ids
 
-    async def get_all(self) -> dict[str, Any]:
-        """Get all data from storage
-
-        Returns:
-            Dictionary containing all stored data
-        """
-        cursor = self._data.find({})
-        result = {}
-        async for doc in cursor:
-            doc_id = doc.pop("_id")
-            # Ensure time fields are present for all documents
-            doc.setdefault("create_time", 0)
-            doc.setdefault("update_time", 0)
-            result[doc_id] = doc
-        return result
-
     async def upsert(self, data: dict[str, dict[str, Any]]) -> None:
         logger.debug(f"[{self.workspace}] Inserting {len(data)} to {self.namespace}")
         if not data:
@@ -236,6 +220,20 @@ class MongoKVStorage(BaseKVStorage):
         # Mongo handles persistence automatically
         pass
 
+    async def is_empty(self) -> bool:
+        """Check if the storage is empty for the current workspace and namespace
+
+        Returns:
+            bool: True if storage is empty, False otherwise
+        """
+        try:
+            # Use count_documents with limit 1 for efficiency
+            count = await self._data.count_documents({}, limit=1)
+            return count == 0
+        except PyMongoError as e:
+            logger.error(f"[{self.workspace}] Error checking if storage is empty: {e}")
+            return True
+
     async def delete(self, ids: list[str]) -> None:
         """Delete documents with specified IDs
 
@@ -466,6 +464,20 @@ class MongoDocStatusStorage(DocStatusStorage):
         # Mongo handles persistence automatically
         pass
 
+    async def is_empty(self) -> bool:
+        """Check if the storage is empty for the current workspace and namespace
+
+        Returns:
+            bool: True if storage is empty, False otherwise
+        """
+        try:
+            # Use count_documents with limit 1 for efficiency
+            count = await self._data.count_documents({}, limit=1)
+            return count == 0
+        except PyMongoError as e:
+            logger.error(f"[{self.workspace}] Error checking if storage is empty: {e}")
+            return True
+
     async def drop(self) -> dict[str, str]:
         """Drop the storage by removing all documents in the collection.
 

lightrag/kg/postgres_impl.py

@@ -1656,113 +1656,6 @@ class PGKVStorage(BaseKVStorage):
                 self.db = None
 
     ################ QUERY METHODS ################
-    async def get_all(self) -> dict[str, Any]:
-        """Get all data from storage
-
-        Returns:
-            Dictionary containing all stored data
-        """
-        table_name = namespace_to_table_name(self.namespace)
-        if not table_name:
-            logger.error(
-                f"[{self.workspace}] Unknown namespace for get_all: {self.namespace}"
-            )
-            return {}
-
-        sql = f"SELECT * FROM {table_name} WHERE workspace=$1"
-        params = {"workspace": self.workspace}
-
-        try:
-            results = await self.db.query(sql, list(params.values()), multirows=True)
-
-            # Special handling for LLM cache to ensure compatibility with _get_cached_extraction_results
-            if is_namespace(self.namespace, NameSpace.KV_STORE_LLM_RESPONSE_CACHE):
-                processed_results = {}
-                for row in results:
-                    create_time = row.get("create_time", 0)
-                    update_time = row.get("update_time", 0)
-                    # Map field names and add cache_type for compatibility
-                    processed_row = {
-                        **row,
-                        "return": row.get("return_value", ""),
-                        "cache_type": row.get("original_prompt", "unknow"),
-                        "original_prompt": row.get("original_prompt", ""),
-                        "chunk_id": row.get("chunk_id"),
-                        "mode": row.get("mode", "default"),
-                        "create_time": create_time,
-                        "update_time": create_time if update_time == 0 else update_time,
-                    }
-                    processed_results[row["id"]] = processed_row
-                return processed_results
-
-            # For text_chunks namespace, parse llm_cache_list JSON string back to list
-            if is_namespace(self.namespace, NameSpace.KV_STORE_TEXT_CHUNKS):
-                processed_results = {}
-                for row in results:
-                    llm_cache_list = row.get("llm_cache_list", [])
-                    if isinstance(llm_cache_list, str):
-                        try:
-                            llm_cache_list = json.loads(llm_cache_list)
-                        except json.JSONDecodeError:
-                            llm_cache_list = []
-                    row["llm_cache_list"] = llm_cache_list
-                    create_time = row.get("create_time", 0)
-                    update_time = row.get("update_time", 0)
-                    row["create_time"] = create_time
-                    row["update_time"] = (
-                        create_time if update_time == 0 else update_time
-                    )
-                    processed_results[row["id"]] = row
-                return processed_results
-
-            # For FULL_ENTITIES namespace, parse entity_names JSON string back to list
-            if is_namespace(self.namespace, NameSpace.KV_STORE_FULL_ENTITIES):
-                processed_results = {}
-                for row in results:
-                    entity_names = row.get("entity_names", [])
-                    if isinstance(entity_names, str):
-                        try:
-                            entity_names = json.loads(entity_names)
-                        except json.JSONDecodeError:
-                            entity_names = []
-                    row["entity_names"] = entity_names
-                    create_time = row.get("create_time", 0)
-                    update_time = row.get("update_time", 0)
-                    row["create_time"] = create_time
-                    row["update_time"] = (
-                        create_time if update_time == 0 else update_time
-                    )
-                    processed_results[row["id"]] = row
-                return processed_results
-
-            # For FULL_RELATIONS namespace, parse relation_pairs JSON string back to list
-            if is_namespace(self.namespace, NameSpace.KV_STORE_FULL_RELATIONS):
-                processed_results = {}
-                for row in results:
-                    relation_pairs = row.get("relation_pairs", [])
-                    if isinstance(relation_pairs, str):
-                        try:
-                            relation_pairs = json.loads(relation_pairs)
-                        except json.JSONDecodeError:
-                            relation_pairs = []
-                    row["relation_pairs"] = relation_pairs
-                    create_time = row.get("create_time", 0)
-                    update_time = row.get("update_time", 0)
-                    row["create_time"] = create_time
-                    row["update_time"] = (
-                        create_time if update_time == 0 else update_time
-                    )
-                    processed_results[row["id"]] = row
-                return processed_results
-
-            # For other namespaces, return as-is
-            return {row["id"]: row for row in results}
-        except Exception as e:
-            logger.error(
-                f"[{self.workspace}] Error retrieving all data from {self.namespace}: {e}"
-            )
-            return {}
-
     async def get_by_id(self, id: str) -> dict[str, Any] | None:
         """Get data by id."""
         sql = SQL_TEMPLATES["get_by_id_" + self.namespace]
@@ -1838,6 +1731,38 @@ class PGKVStorage(BaseKVStorage):
             response["create_time"] = create_time
             response["update_time"] = create_time if update_time == 0 else update_time
 
+        # Special handling for ENTITY_CHUNKS namespace
+        if response and is_namespace(self.namespace, NameSpace.KV_STORE_ENTITY_CHUNKS):
+            # Parse chunk_ids JSON string back to list
+            chunk_ids = response.get("chunk_ids", [])
+            if isinstance(chunk_ids, str):
+                try:
+                    chunk_ids = json.loads(chunk_ids)
+                except json.JSONDecodeError:
+                    chunk_ids = []
+            response["chunk_ids"] = chunk_ids
+            create_time = response.get("create_time", 0)
+            update_time = response.get("update_time", 0)
+            response["create_time"] = create_time
+            response["update_time"] = create_time if update_time == 0 else update_time
+
+        # Special handling for RELATION_CHUNKS namespace
+        if response and is_namespace(
+            self.namespace, NameSpace.KV_STORE_RELATION_CHUNKS
+        ):
+            # Parse chunk_ids JSON string back to list
+            chunk_ids = response.get("chunk_ids", [])
+            if isinstance(chunk_ids, str):
+                try:
+                    chunk_ids = json.loads(chunk_ids)
+                except json.JSONDecodeError:
+                    chunk_ids = []
+            response["chunk_ids"] = chunk_ids
+            create_time = response.get("create_time", 0)
+            update_time = response.get("update_time", 0)
+            response["create_time"] = create_time
+            response["update_time"] = create_time if update_time == 0 else update_time
+
         return response if response else None
 
     # Query by id
@@ -1946,6 +1871,38 @@ class PGKVStorage(BaseKVStorage):
                 result["create_time"] = create_time
                 result["update_time"] = create_time if update_time == 0 else update_time
 
+        # Special handling for ENTITY_CHUNKS namespace
+        if results and is_namespace(self.namespace, NameSpace.KV_STORE_ENTITY_CHUNKS):
+            for result in results:
+                # Parse chunk_ids JSON string back to list
+                chunk_ids = result.get("chunk_ids", [])
+                if isinstance(chunk_ids, str):
+                    try:
+                        chunk_ids = json.loads(chunk_ids)
+                    except json.JSONDecodeError:
+                        chunk_ids = []
+                result["chunk_ids"] = chunk_ids
+                create_time = result.get("create_time", 0)
+                update_time = result.get("update_time", 0)
+                result["create_time"] = create_time
+                result["update_time"] = create_time if update_time == 0 else update_time
+
+        # Special handling for RELATION_CHUNKS namespace
+        if results and is_namespace(self.namespace, NameSpace.KV_STORE_RELATION_CHUNKS):
+            for result in results:
+                # Parse chunk_ids JSON string back to list
+                chunk_ids = result.get("chunk_ids", [])
+                if isinstance(chunk_ids, str):
+                    try:
+                        chunk_ids = json.loads(chunk_ids)
+                    except json.JSONDecodeError:
+                        chunk_ids = []
+                result["chunk_ids"] = chunk_ids
+                create_time = result.get("create_time", 0)
+                update_time = result.get("update_time", 0)
+                result["create_time"] = create_time
+                result["update_time"] = create_time if update_time == 0 else update_time
+
         return _order_results(results)
 
     async def filter_keys(self, keys: set[str]) -> set[str]:
@@ -2050,11 +2007,61 @@ class PGKVStorage(BaseKVStorage):
                     "update_time": current_time,
                 }
                 await self.db.execute(upsert_sql, _data)
+        elif is_namespace(self.namespace, NameSpace.KV_STORE_ENTITY_CHUNKS):
+            # Get current UTC time and convert to naive datetime for database storage
+            current_time = datetime.datetime.now(timezone.utc).replace(tzinfo=None)
+            for k, v in data.items():
+                upsert_sql = SQL_TEMPLATES["upsert_entity_chunks"]
+                _data = {
+                    "workspace": self.workspace,
+                    "id": k,
+                    "chunk_ids": json.dumps(v["chunk_ids"]),
+                    "count": v["count"],
+                    "create_time": current_time,
+                    "update_time": current_time,
+                }
+                await self.db.execute(upsert_sql, _data)
+        elif is_namespace(self.namespace, NameSpace.KV_STORE_RELATION_CHUNKS):
+            # Get current UTC time and convert to naive datetime for database storage
+            current_time = datetime.datetime.now(timezone.utc).replace(tzinfo=None)
+            for k, v in data.items():
+                upsert_sql = SQL_TEMPLATES["upsert_relation_chunks"]
+                _data = {
+                    "workspace": self.workspace,
+                    "id": k,
+                    "chunk_ids": json.dumps(v["chunk_ids"]),
+                    "count": v["count"],
+                    "create_time": current_time,
+                    "update_time": current_time,
+                }
+                await self.db.execute(upsert_sql, _data)
 
     async def index_done_callback(self) -> None:
         # PG handles persistence automatically
         pass
 
+    async def is_empty(self) -> bool:
+        """Check if the storage is empty for the current workspace and namespace
+
+        Returns:
+            bool: True if storage is empty, False otherwise
+        """
+        table_name = namespace_to_table_name(self.namespace)
+        if not table_name:
+            logger.error(
+                f"[{self.workspace}] Unknown namespace for is_empty check: {self.namespace}"
+            )
+            return True
+
+        sql = f"SELECT EXISTS(SELECT 1 FROM {table_name} WHERE workspace=$1 LIMIT 1) as has_data"
+
+        try:
+            result = await self.db.query(sql, [self.workspace])
+            return not result.get("has_data", False) if result else True
+        except Exception as e:
+            logger.error(f"[{self.workspace}] Error checking if storage is empty: {e}")
+            return True
+
     async def delete(self, ids: list[str]) -> None:
         """Delete specific records from storage by their IDs
 
@@ -2970,6 +2977,28 @@ class PGDocStatusStorage(DocStatusStorage):
         # PG handles persistence automatically
         pass
 
+    async def is_empty(self) -> bool:
+        """Check if the storage is empty for the current workspace and namespace
+
+        Returns:
+            bool: True if storage is empty, False otherwise
+        """
+        table_name = namespace_to_table_name(self.namespace)
+        if not table_name:
+            logger.error(
+                f"[{self.workspace}] Unknown namespace for is_empty check: {self.namespace}"
+            )
+            return True
+
+        sql = f"SELECT EXISTS(SELECT 1 FROM {table_name} WHERE workspace=$1 LIMIT 1) as has_data"
+
+        try:
+            result = await self.db.query(sql, [self.workspace])
+            return not result.get("has_data", False) if result else True
+        except Exception as e:
+            logger.error(f"[{self.workspace}] Error checking if storage is empty: {e}")
+            return True
+
     async def delete(self, ids: list[str]) -> None:
         """Delete specific records from storage by their IDs
 
@@ -4721,6 +4750,8 @@ NAMESPACE_TABLE_MAP = {
     NameSpace.KV_STORE_TEXT_CHUNKS: "LIGHTRAG_DOC_CHUNKS",
     NameSpace.KV_STORE_FULL_ENTITIES: "LIGHTRAG_FULL_ENTITIES",
     NameSpace.KV_STORE_FULL_RELATIONS: "LIGHTRAG_FULL_RELATIONS",
+    NameSpace.KV_STORE_ENTITY_CHUNKS: "LIGHTRAG_ENTITY_CHUNKS",
+    NameSpace.KV_STORE_RELATION_CHUNKS: "LIGHTRAG_RELATION_CHUNKS",
     NameSpace.KV_STORE_LLM_RESPONSE_CACHE: "LIGHTRAG_LLM_CACHE",
     NameSpace.VECTOR_STORE_CHUNKS: "LIGHTRAG_VDB_CHUNKS",
     NameSpace.VECTOR_STORE_ENTITIES: "LIGHTRAG_VDB_ENTITY",
@@ -4861,6 +4892,28 @@ TABLES = {
                     CONSTRAINT LIGHTRAG_FULL_RELATIONS_PK PRIMARY KEY (workspace, id)
                     )"""
     },
+    "LIGHTRAG_ENTITY_CHUNKS": {
+        "ddl": """CREATE TABLE LIGHTRAG_ENTITY_CHUNKS (
+                    id VARCHAR(512),
+                    workspace VARCHAR(255),
+                    chunk_ids JSONB,
+                    count INTEGER,
+                    create_time TIMESTAMP(0) DEFAULT CURRENT_TIMESTAMP,
+                    update_time TIMESTAMP(0) DEFAULT CURRENT_TIMESTAMP,
+                    CONSTRAINT LIGHTRAG_ENTITY_CHUNKS_PK PRIMARY KEY (workspace, id)
+                    )"""
+    },
+    "LIGHTRAG_RELATION_CHUNKS": {
+        "ddl": """CREATE TABLE LIGHTRAG_RELATION_CHUNKS (
+                    id VARCHAR(512),
+                    workspace VARCHAR(255),
+                    chunk_ids JSONB,
+                    count INTEGER,
+                    create_time TIMESTAMP(0) DEFAULT CURRENT_TIMESTAMP,
+                    update_time TIMESTAMP(0) DEFAULT CURRENT_TIMESTAMP,
+                    CONSTRAINT LIGHTRAG_RELATION_CHUNKS_PK PRIMARY KEY (workspace, id)
+                    )"""
+    },
 }
 
 
@@ -4918,6 +4971,26 @@ SQL_TEMPLATES = {
                                  EXTRACT(EPOCH FROM update_time)::BIGINT as update_time
                                  FROM LIGHTRAG_FULL_RELATIONS WHERE workspace=$1 AND id = ANY($2)
                                 """,
+    "get_by_id_entity_chunks": """SELECT id, chunk_ids, count,
+                                EXTRACT(EPOCH FROM create_time)::BIGINT as create_time,
+                                EXTRACT(EPOCH FROM update_time)::BIGINT as update_time
+                                FROM LIGHTRAG_ENTITY_CHUNKS WHERE workspace=$1 AND id=$2
+                               """,
+    "get_by_id_relation_chunks": """SELECT id, chunk_ids, count,
+                                EXTRACT(EPOCH FROM create_time)::BIGINT as create_time,
+                                EXTRACT(EPOCH FROM update_time)::BIGINT as update_time
+                                FROM LIGHTRAG_RELATION_CHUNKS WHERE workspace=$1 AND id=$2
+                               """,
+    "get_by_ids_entity_chunks": """SELECT id, chunk_ids, count,
+                                 EXTRACT(EPOCH FROM create_time)::BIGINT as create_time,
+                                 EXTRACT(EPOCH FROM update_time)::BIGINT as update_time
+                                 FROM LIGHTRAG_ENTITY_CHUNKS WHERE workspace=$1 AND id = ANY($2)
+                                """,
+    "get_by_ids_relation_chunks": """SELECT id, chunk_ids, count,
+                                 EXTRACT(EPOCH FROM create_time)::BIGINT as create_time,
+                                 EXTRACT(EPOCH FROM update_time)::BIGINT as update_time
+                                 FROM LIGHTRAG_RELATION_CHUNKS WHERE workspace=$1 AND id = ANY($2)
+                                """,
     "filter_keys": "SELECT id FROM {table_name} WHERE workspace=$1 AND id IN ({ids})",
     "upsert_doc_full": """INSERT INTO LIGHTRAG_DOC_FULL (id, content, doc_name, workspace)
                         VALUES ($1, $2, $3, $4)
@@ -4965,6 +5038,22 @@ SQL_TEMPLATES = {
                       count=EXCLUDED.count,
                       update_time = EXCLUDED.update_time
                      """,
+    "upsert_entity_chunks": """INSERT INTO LIGHTRAG_ENTITY_CHUNKS (workspace, id, chunk_ids, count,
+                      create_time, update_time)
+                      VALUES ($1, $2, $3, $4, $5, $6)
+                      ON CONFLICT (workspace,id) DO UPDATE
+                      SET chunk_ids=EXCLUDED.chunk_ids,
+                      count=EXCLUDED.count,
+                      update_time = EXCLUDED.update_time
+                     """,
+    "upsert_relation_chunks": """INSERT INTO LIGHTRAG_RELATION_CHUNKS (workspace, id, chunk_ids, count,
+                      create_time, update_time)
+                      VALUES ($1, $2, $3, $4, $5, $6)
+                      ON CONFLICT (workspace,id) DO UPDATE
+                      SET chunk_ids=EXCLUDED.chunk_ids,
+                      count=EXCLUDED.count,
+                      update_time = EXCLUDED.update_time
+                     """,
     # SQL for VectorStorage
     "upsert_chunk": """INSERT INTO LIGHTRAG_VDB_CHUNKS (workspace, id, tokens,
                       chunk_order_index, full_doc_id, content, content_vector, file_path,

lightrag/kg/redis_impl.py

@@ -304,51 +304,6 @@ class RedisKVStorage(BaseKVStorage):
                 logger.error(f"[{self.workspace}] JSON decode error in batch get: {e}")
                 return [None] * len(ids)
 
-    async def get_all(self) -> dict[str, Any]:
-        """Get all data from storage
-
-        Returns:
-            Dictionary containing all stored data
-        """
-        async with self._get_redis_connection() as redis:
-            try:
-                # Get all keys for this namespace
-                keys = await redis.keys(f"{self.final_namespace}:*")
-
-                if not keys:
-                    return {}
-
-                # Get all values in batch
-                pipe = redis.pipeline()
-                for key in keys:
-                    pipe.get(key)
-                values = await pipe.execute()
-
-                # Build result dictionary
-                result = {}
-                for key, value in zip(keys, values):
-                    if value:
-                        # Extract the ID part (after namespace:)
-                        key_id = key.split(":", 1)[1]
-                        try:
-                            data = json.loads(value)
-                            # Ensure time fields are present for all documents
-                            data.setdefault("create_time", 0)
-                            data.setdefault("update_time", 0)
-                            result[key_id] = data
-                        except json.JSONDecodeError as e:
-                            logger.error(
-                                f"[{self.workspace}] JSON decode error for key {key}: {e}"
-                            )
-                            continue
-
-                return result
-            except Exception as e:
-                logger.error(
-                    f"[{self.workspace}] Error getting all data from Redis: {e}"
-                )
-                return {}
-
     async def filter_keys(self, keys: set[str]) -> set[str]:
         async with self._get_redis_connection() as redis:
             pipe = redis.pipeline()
@@ -407,8 +362,24 @@ class RedisKVStorage(BaseKVStorage):
         # Redis handles persistence automatically
         pass
 
+    async def is_empty(self) -> bool:
+        """Check if the storage is empty for the current workspace and namespace
+
+        Returns:
+            bool: True if storage is empty, False otherwise
+        """
+        pattern = f"{self.namespace}:{self.workspace}:*"
+        try:
+            # Use scan to check if any keys exist
+            async for key in self.redis.scan_iter(match=pattern, count=1):
+                return False  # Found at least one key
+            return True  # No keys found
+        except Exception as e:
+            logger.error(f"[{self.workspace}] Error checking if storage is empty: {e}")
+            return True
+
     async def delete(self, ids: list[str]) -> None:
-        """Delete entries with specified IDs"""
+        """Delete specific records from storage by their IDs"""
         if not ids:
             return
 
@@ -868,6 +839,23 @@ class RedisDocStatusStorage(DocStatusStorage):
         """Redis handles persistence automatically"""
         pass
 
+    async def is_empty(self) -> bool:
+        """Check if the storage is empty for the current workspace and namespace
+
+        Returns:
+            bool: True if storage is empty, False otherwise
+        """
+        pattern = f"{self.final_namespace}:*"
+        try:
+            async with self._get_redis_connection() as redis:
+                # Use scan to check if any keys exist
+                async for key in redis.scan_iter(match=pattern, count=1):
+                    return False  # Found at least one key
+                return True  # No keys found
+        except Exception as e:
+            logger.error(f"[{self.workspace}] Error checking if storage is empty: {e}")
+            return True
+
     @redis_retry
     async def upsert(self, data: dict[str, dict[str, Any]]) -> None:
         """Insert or update document status data"""

lightrag/lightrag.py

@@ -41,10 +41,12 @@ from lightrag.constants import (
     DEFAULT_MAX_PARALLEL_INSERT,
     DEFAULT_MAX_GRAPH_NODES,
     DEFAULT_MAX_SOURCE_IDS_PER_ENTITY,
+    DEFAULT_MAX_SOURCE_IDS_PER_RELATION,
     DEFAULT_ENTITY_TYPES,
     DEFAULT_SUMMARY_LANGUAGE,
     DEFAULT_LLM_TIMEOUT,
     DEFAULT_EMBEDDING_TIMEOUT,
+    DEFAULT_SOURCE_IDS_LIMIT_METHOD,
 )
 from lightrag.utils import get_env_value
 
@@ -99,6 +101,9 @@ from lightrag.utils import (
     generate_track_id,
     convert_to_user_format,
     logger,
+    subtract_source_ids,
+    make_relation_chunk_key,
+    normalize_source_ids_limit_method,
 )
 from lightrag.types import KnowledgeGraph
 from dotenv import load_dotenv
@@ -362,10 +367,32 @@ class LightRAG:
     """Maximum number of graph nodes to return in knowledge graph queries."""
 
     max_source_ids_per_entity: int = field(
-        default=get_env_value("MAX_SOURCE_IDS_PER_ENTITY", DEFAULT_MAX_SOURCE_IDS_PER_ENTITY, int)
+        default=get_env_value(
+            "MAX_SOURCE_IDS_PER_ENTITY", DEFAULT_MAX_SOURCE_IDS_PER_ENTITY, int
+        )
     )
     """Maximum number of source (chunk) ids in entity Grpah + VDB."""
 
+    max_source_ids_per_relation: int = field(
+        default=get_env_value(
+            "MAX_SOURCE_IDS_PER_RELATION",
+            DEFAULT_MAX_SOURCE_IDS_PER_RELATION,
+            int,
+        )
+    )
+    """Maximum number of source (chunk) ids in relation Graph + VDB."""
+
+    source_ids_limit_method: str = field(
+        default_factory=lambda: normalize_source_ids_limit_method(
+            get_env_value(
+                "SOURCE_IDS_LIMIT_METHOD",
+                DEFAULT_SOURCE_IDS_LIMIT_METHOD,
+                str,
+            )
+        )
+    )
+    """Strategy for enforcing source_id limits: IGNORE_NEW or FIFO."""
+
     addon_params: dict[str, Any] = field(
         default_factory=lambda: {
             "language": get_env_value(
@@ -535,6 +562,18 @@ class LightRAG:
             embedding_func=self.embedding_func,
         )
 
+        self.entity_chunks: BaseKVStorage = self.key_string_value_json_storage_cls(  # type: ignore
+            namespace=NameSpace.KV_STORE_ENTITY_CHUNKS,
+            workspace=self.workspace,
+            embedding_func=self.embedding_func,
+        )
+
+        self.relation_chunks: BaseKVStorage = self.key_string_value_json_storage_cls(  # type: ignore
+            namespace=NameSpace.KV_STORE_RELATION_CHUNKS,
+            workspace=self.workspace,
+            embedding_func=self.embedding_func,
+        )
+
         self.chunk_entity_relation_graph: BaseGraphStorage = self.graph_storage_cls(  # type: ignore
             namespace=NameSpace.GRAPH_STORE_CHUNK_ENTITY_RELATION,
             workspace=self.workspace,
@@ -594,6 +633,8 @@ class LightRAG:
                 self.text_chunks,
                 self.full_entities,
                 self.full_relations,
+                self.entity_chunks,
+                self.relation_chunks,
                 self.entities_vdb,
                 self.relationships_vdb,
                 self.chunks_vdb,
@@ -616,6 +657,8 @@ class LightRAG:
                 ("text_chunks", self.text_chunks),
                 ("full_entities", self.full_entities),
                 ("full_relations", self.full_relations),
+                ("entity_chunks", self.entity_chunks),
+                ("relation_chunks", self.relation_chunks),
                 ("entities_vdb", self.entities_vdb),
                 ("relationships_vdb", self.relationships_vdb),
                 ("chunks_vdb", self.chunks_vdb),
@@ -671,6 +714,13 @@ class LightRAG:
                     logger.debug("No entities found in graph, skipping migration check")
                     return
 
+                try:
+                    # Initialize chunk tracking storage after migration
+                    await self._migrate_chunk_tracking_storage()
+                except Exception as e:
+                    logger.error(f"Error during chunk_tracking migration: {e}")
+                    raise e
+
                 # Check if full_entities and full_relations are empty
                 # Get all processed documents to check their entity/relation data
                 try:
@@ -711,11 +761,11 @@ class LightRAG:
 
                 except Exception as e:
                     logger.error(f"Error during migration check: {e}")
-                    # Don't raise the error, just log it to avoid breaking initialization
+                    raise e
 
             except Exception as e:
                 logger.error(f"Error in data migration check: {e}")
-                # Don't raise the error to avoid breaking initialization
+                raise e
 
     async def _migrate_entity_relation_data(self, processed_docs: dict):
         """Migrate existing entity and relation data to full_entities and full_relations storage"""
@@ -814,6 +864,140 @@ class LightRAG:
             f"Data migration completed: migrated {migration_count} documents with entities/relations"
         )
 
+    async def _migrate_chunk_tracking_storage(self) -> None:
+        """Ensure entity/relation chunk tracking KV stores exist and are seeded."""
+
+        if not self.entity_chunks or not self.relation_chunks:
+            return
+
+        need_entity_migration = False
+        need_relation_migration = False
+
+        try:
+            need_entity_migration = await self.entity_chunks.is_empty()
+        except Exception as exc:  # pragma: no cover - defensive logging
+            logger.error(f"Failed to check entity chunks storage: {exc}")
+            need_entity_migration = True
+
+        try:
+            need_relation_migration = await self.relation_chunks.is_empty()
+        except Exception as exc:  # pragma: no cover - defensive logging
+            logger.error(f"Failed to check relation chunks storage: {exc}")
+            need_relation_migration = True
+
+        if not need_entity_migration and not need_relation_migration:
+            return
+
+        BATCH_SIZE = 500  # Process 500 records per batch
+
+        if need_entity_migration:
+            try:
+                nodes = await self.chunk_entity_relation_graph.get_all_nodes()
+            except Exception as exc:
+                logger.error(f"Failed to fetch nodes for chunk migration: {exc}")
+                nodes = []
+
+            logger.info(f"Starting chunk_tracking data migration: {len(nodes)} nodes")
+
+            # Process nodes in batches
+            total_nodes = len(nodes)
+            total_batches = (total_nodes + BATCH_SIZE - 1) // BATCH_SIZE
+            total_migrated = 0
+
+            for batch_idx in range(total_batches):
+                start_idx = batch_idx * BATCH_SIZE
+                end_idx = min((batch_idx + 1) * BATCH_SIZE, total_nodes)
+                batch_nodes = nodes[start_idx:end_idx]
+
+                upsert_payload: dict[str, dict[str, object]] = {}
+                for node in batch_nodes:
+                    entity_id = node.get("entity_id") or node.get("id")
+                    if not entity_id:
+                        continue
+
+                    raw_source = node.get("source_id") or ""
+                    chunk_ids = [
+                        chunk_id
+                        for chunk_id in raw_source.split(GRAPH_FIELD_SEP)
+                        if chunk_id
+                    ]
+                    if not chunk_ids:
+                        continue
+
+                    upsert_payload[entity_id] = {
+                        "chunk_ids": chunk_ids,
+                        "count": len(chunk_ids),
+                    }
+
+                if upsert_payload:
+                    await self.entity_chunks.upsert(upsert_payload)
+                    total_migrated += len(upsert_payload)
+                    logger.info(
+                        f"Processed entity batch {batch_idx + 1}/{total_batches}: {len(upsert_payload)} records (total: {total_migrated}/{total_nodes})"
+                    )
+
+            if total_migrated > 0:
+                # Persist entity_chunks data to disk
+                await self.entity_chunks.index_done_callback()
+                logger.info(
+                    f"Entity chunk_tracking migration completed: {total_migrated} records persisted"
+                )
+
+        if need_relation_migration:
+            try:
+                edges = await self.chunk_entity_relation_graph.get_all_edges()
+            except Exception as exc:
+                logger.error(f"Failed to fetch edges for chunk migration: {exc}")
+                edges = []
+
+            logger.info(f"Starting chunk_tracking data migration: {len(edges)} edges")
+
+            # Process edges in batches
+            total_edges = len(edges)
+            total_batches = (total_edges + BATCH_SIZE - 1) // BATCH_SIZE
+            total_migrated = 0
+
+            for batch_idx in range(total_batches):
+                start_idx = batch_idx * BATCH_SIZE
+                end_idx = min((batch_idx + 1) * BATCH_SIZE, total_edges)
+                batch_edges = edges[start_idx:end_idx]
+
+                upsert_payload: dict[str, dict[str, object]] = {}
+                for edge in batch_edges:
+                    src = edge.get("source") or edge.get("src_id") or edge.get("src")
+                    tgt = edge.get("target") or edge.get("tgt_id") or edge.get("tgt")
+                    if not src or not tgt:
+                        continue
+
+                    raw_source = edge.get("source_id") or ""
+                    chunk_ids = [
+                        chunk_id
+                        for chunk_id in raw_source.split(GRAPH_FIELD_SEP)
+                        if chunk_id
+                    ]
+                    if not chunk_ids:
+                        continue
+
+                    storage_key = make_relation_chunk_key(src, tgt)
+                    upsert_payload[storage_key] = {
+                        "chunk_ids": chunk_ids,
+                        "count": len(chunk_ids),
+                    }
+
+                if upsert_payload:
+                    await self.relation_chunks.upsert(upsert_payload)
+                    total_migrated += len(upsert_payload)
+                    logger.info(
+                        f"Processed relation batch {batch_idx + 1}/{total_batches}: {len(upsert_payload)} records (total: {total_migrated}/{total_edges})"
+                    )
+
+            if total_migrated > 0:
+                # Persist relation_chunks data to disk
+                await self.relation_chunks.index_done_callback()
+                logger.info(
+                    f"Relation chunk_tracking migration completed: {total_migrated} records persisted"
+                )
+
     async def get_graph_labels(self):
         text = await self.chunk_entity_relation_graph.get_all_labels()
         return text
@@ -1676,6 +1860,8 @@ class LightRAG:
                                     pipeline_status=pipeline_status,
                                     pipeline_status_lock=pipeline_status_lock,
                                     llm_response_cache=self.llm_response_cache,
+                                    entity_chunks_storage=self.entity_chunks,
+                                    relation_chunks_storage=self.relation_chunks,
                                     current_file_number=current_file_number,
                                     total_files=total_files,
                                     file_path=file_path,
@@ -1845,6 +2031,8 @@ class LightRAG:
                 self.text_chunks,
                 self.full_entities,
                 self.full_relations,
+                self.entity_chunks,
+                self.relation_chunks,
                 self.llm_response_cache,
                 self.entities_vdb,
                 self.relationships_vdb,
@@ -2718,9 +2906,11 @@ class LightRAG:
 
             # 4. Analyze entities and relationships that will be affected
             entities_to_delete = set()
-            entities_to_rebuild = {}  # entity_name -> remaining_chunk_ids
+            entities_to_rebuild = {}  # entity_name -> remaining chunk id list
             relationships_to_delete = set()
-            relationships_to_rebuild = {}  # (src, tgt) -> remaining_chunk_ids
+            relationships_to_rebuild = {}  # (src, tgt) -> remaining chunk id list
+            entity_chunk_updates: dict[str, list[str]] = {}
+            relation_chunk_updates: dict[tuple[str, str], list[str]] = {}
 
             try:
                 # Get affected entities and relations from full_entities and full_relations storage
@@ -2776,14 +2966,41 @@ class LightRAG:
                 # Process entities
                 for node_data in affected_nodes:
                     node_label = node_data.get("entity_id")
-                    if node_label and "source_id" in node_data:
+                    if not node_label:
-                        sources = set(node_data["source_id"].split(GRAPH_FIELD_SEP))
+                        continue
-                        remaining_sources = sources - chunk_ids
+
+                    existing_sources: list[str] = []
+                    if self.entity_chunks:
+                        stored_chunks = await self.entity_chunks.get_by_id(node_label)
+                        if stored_chunks and isinstance(stored_chunks, dict):
+                            existing_sources = [
+                                chunk_id
+                                for chunk_id in stored_chunks.get("chunk_ids", [])
+                                if chunk_id
+                            ]
+
+                    if not existing_sources and node_data.get("source_id"):
+                        existing_sources = [
+                            chunk_id
+                            for chunk_id in node_data["source_id"].split(
+                                GRAPH_FIELD_SEP
+                            )
+                            if chunk_id
+                        ]
+
+                    if not existing_sources:
+                        continue
+
+                    remaining_sources = subtract_source_ids(existing_sources, chunk_ids)
 
                     if not remaining_sources:
                         entities_to_delete.add(node_label)
-                        elif remaining_sources != sources:
+                        entity_chunk_updates[node_label] = []
+                    elif remaining_sources != existing_sources:
                         entities_to_rebuild[node_label] = remaining_sources
+                        entity_chunk_updates[node_label] = remaining_sources
+                    else:
+                        logger.info(f"Untouch entity: {node_label}")
 
                 async with pipeline_status_lock:
                     log_message = f"Found {len(entities_to_rebuild)} affected entities"
@@ -2796,7 +3013,9 @@ class LightRAG:
                     src = edge_data.get("source")
                     tgt = edge_data.get("target")
 
-                    if src and tgt and "source_id" in edge_data:
+                    if not src or not tgt or "source_id" not in edge_data:
+                        continue
+
                     edge_tuple = tuple(sorted((src, tgt)))
                     if (
                         edge_tuple in relationships_to_delete
@@ -2804,13 +3023,41 @@ class LightRAG:
                     ):
                         continue
 
-                        sources = set(edge_data["source_id"].split(GRAPH_FIELD_SEP))
+                    existing_sources: list[str] = []
-                        remaining_sources = sources - chunk_ids
+                    if self.relation_chunks:
+                        storage_key = make_relation_chunk_key(src, tgt)
+                        stored_chunks = await self.relation_chunks.get_by_id(
+                            storage_key
+                        )
+                        if stored_chunks and isinstance(stored_chunks, dict):
+                            existing_sources = [
+                                chunk_id
+                                for chunk_id in stored_chunks.get("chunk_ids", [])
+                                if chunk_id
+                            ]
+
+                    if not existing_sources:
+                        existing_sources = [
+                            chunk_id
+                            for chunk_id in edge_data["source_id"].split(
+                                GRAPH_FIELD_SEP
+                            )
+                            if chunk_id
+                        ]
+
+                    if not existing_sources:
+                        continue
+
+                    remaining_sources = subtract_source_ids(existing_sources, chunk_ids)
 
                     if not remaining_sources:
                         relationships_to_delete.add(edge_tuple)
-                        elif remaining_sources != sources:
+                        relation_chunk_updates[edge_tuple] = []
+                    elif remaining_sources != existing_sources:
                         relationships_to_rebuild[edge_tuple] = remaining_sources
+                        relation_chunk_updates[edge_tuple] = remaining_sources
+                    else:
+                        logger.info(f"Untouch relation: {edge_tuple}")
 
                 async with pipeline_status_lock:
                     log_message = (
@@ -2820,6 +3067,45 @@ class LightRAG:
                     pipeline_status["latest_message"] = log_message
                     pipeline_status["history_messages"].append(log_message)
 
+                current_time = int(time.time())
+
+                if entity_chunk_updates and self.entity_chunks:
+                    entity_upsert_payload = {}
+                    entity_delete_ids: set[str] = set()
+                    for entity_name, remaining in entity_chunk_updates.items():
+                        if not remaining:
+                            entity_delete_ids.add(entity_name)
+                        else:
+                            entity_upsert_payload[entity_name] = {
+                                "chunk_ids": remaining,
+                                "count": len(remaining),
+                                "updated_at": current_time,
+                            }
+
+                    if entity_delete_ids:
+                        await self.entity_chunks.delete(list(entity_delete_ids))
+                    if entity_upsert_payload:
+                        await self.entity_chunks.upsert(entity_upsert_payload)
+
+                if relation_chunk_updates and self.relation_chunks:
+                    relation_upsert_payload = {}
+                    relation_delete_ids: set[str] = set()
+                    for edge_tuple, remaining in relation_chunk_updates.items():
+                        storage_key = make_relation_chunk_key(*edge_tuple)
+                        if not remaining:
+                            relation_delete_ids.add(storage_key)
+                        else:
+                            relation_upsert_payload[storage_key] = {
+                                "chunk_ids": remaining,
+                                "count": len(remaining),
+                                "updated_at": current_time,
+                            }
+
+                    if relation_delete_ids:
+                        await self.relation_chunks.delete(list(relation_delete_ids))
+                    if relation_upsert_payload:
+                        await self.relation_chunks.upsert(relation_upsert_payload)
+
             except Exception as e:
                 logger.error(f"Failed to process graph analysis results: {e}")
                 raise Exception(f"Failed to process graph dependencies: {e}") from e
@@ -2914,6 +3200,8 @@ class LightRAG:
                         global_config=asdict(self),
                         pipeline_status=pipeline_status,
                         pipeline_status_lock=pipeline_status_lock,
+                        entity_chunks_storage=self.entity_chunks,
+                        relation_chunks_storage=self.relation_chunks,
                     )
 
                 except Exception as e:

lightrag/namespace.py

@@ -10,6 +10,8 @@ class NameSpace:
     KV_STORE_LLM_RESPONSE_CACHE = "llm_response_cache"
     KV_STORE_FULL_ENTITIES = "full_entities"
     KV_STORE_FULL_RELATIONS = "full_relations"
+    KV_STORE_ENTITY_CHUNKS = "entity_chunks"
+    KV_STORE_RELATION_CHUNKS = "relation_chunks"
 
     VECTOR_STORE_ENTITIES = "entities"
     VECTOR_STORE_RELATIONSHIPS = "relationships"

lightrag/operate.py

@@ -7,7 +7,7 @@ import json_repair
 from typing import Any, AsyncIterator, overload, Literal
 from collections import Counter, defaultdict
 
-from .utils import (
+from lightrag.utils import (
     logger,
     compute_mdhash_id,
     Tokenizer,
@@ -27,14 +27,16 @@ from .utils import (
     pick_by_vector_similarity,
     process_chunks_unified,
     build_file_path,
-    truncate_entity_source_id,
     safe_vdb_operation_with_exception,
     create_prefixed_exception,
     fix_tuple_delimiter_corruption,
     convert_to_user_format,
     generate_reference_list_from_chunks,
+    apply_source_ids_limit,
+    merge_source_ids,
+    make_relation_chunk_key,
 )
-from .base import (
+from lightrag.base import (
     BaseGraphStorage,
     BaseKVStorage,
     BaseVectorStorage,
@@ -43,8 +45,8 @@ from .base import (
     QueryResult,
     QueryContextResult,
 )
-from .prompt import PROMPTS
+from lightrag.prompt import PROMPTS
-from .constants import (
+from lightrag.constants import (
     GRAPH_FIELD_SEP,
     DEFAULT_MAX_ENTITY_TOKENS,
     DEFAULT_MAX_RELATION_TOKENS,
@@ -53,8 +55,9 @@ from .constants import (
     DEFAULT_KG_CHUNK_PICK_METHOD,
     DEFAULT_ENTITY_TYPES,
     DEFAULT_SUMMARY_LANGUAGE,
+    SOURCE_IDS_LIMIT_METHOD_KEEP,
 )
-from .kg.shared_storage import get_storage_keyed_lock
+from lightrag.kg.shared_storage import get_storage_keyed_lock
 import time
 from dotenv import load_dotenv
 
@@ -474,8 +477,8 @@ async def _handle_single_relationship_extraction(
 
 
 async def _rebuild_knowledge_from_chunks(
-    entities_to_rebuild: dict[str, set[str]],
+    entities_to_rebuild: dict[str, list[str]],
-    relationships_to_rebuild: dict[tuple[str, str], set[str]],
+    relationships_to_rebuild: dict[tuple[str, str], list[str]],
     knowledge_graph_inst: BaseGraphStorage,
     entities_vdb: BaseVectorStorage,
     relationships_vdb: BaseVectorStorage,
@@ -484,6 +487,8 @@ async def _rebuild_knowledge_from_chunks(
     global_config: dict[str, str],
     pipeline_status: dict | None = None,
     pipeline_status_lock=None,
+    entity_chunks_storage: BaseKVStorage | None = None,
+    relation_chunks_storage: BaseKVStorage | None = None,
 ) -> None:
     """Rebuild entity and relationship descriptions from cached extraction results with parallel processing
 
@@ -492,8 +497,8 @@ async def _rebuild_knowledge_from_chunks(
     controlled by llm_model_max_async and using get_storage_keyed_lock for data consistency.
 
     Args:
-        entities_to_rebuild: Dict mapping entity_name -> set of remaining chunk_ids
+        entities_to_rebuild: Dict mapping entity_name -> list of remaining chunk_ids
-        relationships_to_rebuild: Dict mapping (src, tgt) -> set of remaining chunk_ids
+        relationships_to_rebuild: Dict mapping (src, tgt) -> list of remaining chunk_ids
         knowledge_graph_inst: Knowledge graph storage
         entities_vdb: Entity vector database
         relationships_vdb: Relationship vector database
@@ -502,6 +507,8 @@ async def _rebuild_knowledge_from_chunks(
         global_config: Global configuration containing llm_model_max_async
         pipeline_status: Pipeline status dictionary
         pipeline_status_lock: Lock for pipeline status
+        entity_chunks_storage: KV storage maintaining full chunk IDs per entity
+        relation_chunks_storage: KV storage maintaining full chunk IDs per relation
     """
     if not entities_to_rebuild and not relationships_to_rebuild:
         return
@@ -641,10 +648,11 @@ async def _rebuild_knowledge_from_chunks(
                         chunk_entities=chunk_entities,
                         llm_response_cache=llm_response_cache,
                         global_config=global_config,
+                        entity_chunks_storage=entity_chunks_storage,
                     )
                     rebuilt_entities_count += 1
                     status_message = (
-                        f"Rebuilt `{entity_name}` from {len(chunk_ids)} chunks"
+                        f"Rebuild `{entity_name}` from {len(chunk_ids)} chunks"
                     )
                     logger.info(status_message)
                     if pipeline_status is not None and pipeline_status_lock is not None:
@@ -682,16 +690,11 @@ async def _rebuild_knowledge_from_chunks(
                         chunk_relationships=chunk_relationships,
                         llm_response_cache=llm_response_cache,
                         global_config=global_config,
+                        relation_chunks_storage=relation_chunks_storage,
+                        pipeline_status=pipeline_status,
+                        pipeline_status_lock=pipeline_status_lock,
                     )
                     rebuilt_relationships_count += 1
-                    status_message = (
-                        f"Rebuilt `{src} - {tgt}` from {len(chunk_ids)} chunks"
-                    )
-                    logger.info(status_message)
-                    if pipeline_status is not None and pipeline_status_lock is not None:
-                        async with pipeline_status_lock:
-                            pipeline_status["latest_message"] = status_message
-                            pipeline_status["history_messages"].append(status_message)
                 except Exception as e:
                     failed_relationships_count += 1
                     status_message = f"Failed to rebuild `{src} - {tgt}`: {e}"
@@ -1002,10 +1005,13 @@ async def _rebuild_single_entity(
     knowledge_graph_inst: BaseGraphStorage,
     entities_vdb: BaseVectorStorage,
     entity_name: str,
-    chunk_ids: set[str],
+    chunk_ids: list[str],
     chunk_entities: dict,
     llm_response_cache: BaseKVStorage,
     global_config: dict[str, str],
+    entity_chunks_storage: BaseKVStorage | None = None,
+    pipeline_status: dict | None = None,
+    pipeline_status_lock=None,
 ) -> None:
     """Rebuild a single entity from cached extraction results"""
 
@@ -1016,7 +1022,11 @@ async def _rebuild_single_entity(
 
     # Helper function to update entity in both graph and vector storage
     async def _update_entity_storage(
-        final_description: str, entity_type: str, file_paths: set[str]
+        final_description: str,
+        entity_type: str,
+        file_paths: set[str],
+        source_chunk_ids: list[str],
+        truncation_info: str = "",
     ):
         try:
             # Update entity in graph storage (critical path)
@@ -1024,10 +1034,12 @@ async def _rebuild_single_entity(
                 **current_entity,
                 "description": final_description,
                 "entity_type": entity_type,
-                "source_id": GRAPH_FIELD_SEP.join(chunk_ids),
+                "source_id": GRAPH_FIELD_SEP.join(source_chunk_ids),
                 "file_path": GRAPH_FIELD_SEP.join(file_paths)
                 if file_paths
                 else current_entity.get("file_path", "unknown_source"),
+                "created_at": int(time.time()),
+                "truncate": truncation_info,
             }
             await knowledge_graph_inst.upsert_node(entity_name, updated_entity_data)
 
@@ -1060,9 +1072,33 @@ async def _rebuild_single_entity(
             logger.error(error_msg)
             raise  # Re-raise exception
 
-    # Collect all entity data from relevant chunks
+    # normalized_chunk_ids = merge_source_ids([], chunk_ids)
+    normalized_chunk_ids = chunk_ids
+
+    if entity_chunks_storage is not None and normalized_chunk_ids:
+        await entity_chunks_storage.upsert(
+            {
+                entity_name: {
+                    "chunk_ids": normalized_chunk_ids,
+                    "count": len(normalized_chunk_ids),
+                }
+            }
+        )
+
+    limit_method = (
+        global_config.get("source_ids_limit_method") or SOURCE_IDS_LIMIT_METHOD_KEEP
+    )
+
+    limited_chunk_ids = apply_source_ids_limit(
+        normalized_chunk_ids,
+        global_config["max_source_ids_per_entity"],
+        limit_method,
+        identifier=f"`{entity_name}`",
+    )
+
+    # Collect all entity data from relevant (limited) chunks
     all_entity_data = []
-    for chunk_id in chunk_ids:
+    for chunk_id in limited_chunk_ids:
         if chunk_id in chunk_entities and entity_name in chunk_entities[chunk_id]:
             all_entity_data.extend(chunk_entities[chunk_id][entity_name])
 
@@ -1109,7 +1145,12 @@ async def _rebuild_single_entity(
             final_description = current_entity.get("description", "")
 
         entity_type = current_entity.get("entity_type", "UNKNOWN")
-        await _update_entity_storage(final_description, entity_type, file_paths)
+        await _update_entity_storage(
+            final_description,
+            entity_type,
+            file_paths,
+            limited_chunk_ids,
+        )
         return
 
     # Process cached entity data
@@ -1149,7 +1190,31 @@ async def _rebuild_single_entity(
     else:
         final_description = current_entity.get("description", "")
 
-    await _update_entity_storage(final_description, entity_type, file_paths)
+    if len(limited_chunk_ids) < len(normalized_chunk_ids):
+        truncation_info = (
+            f"{limit_method}:{len(limited_chunk_ids)}/{len(normalized_chunk_ids)}"
+        )
+    else:
+        truncation_info = ""
+
+    await _update_entity_storage(
+        final_description,
+        entity_type,
+        file_paths,
+        limited_chunk_ids,
+        truncation_info,
+    )
+
+    # Log rebuild completion with truncation info
+    status_message = f"Rebuild `{entity_name}` from {len(chunk_ids)} chunks"
+    if truncation_info:
+        status_message += f" ({truncation_info})"
+    logger.info(status_message)
+    # Update pipeline status
+    if pipeline_status is not None and pipeline_status_lock is not None:
+        async with pipeline_status_lock:
+            pipeline_status["latest_message"] = status_message
+            pipeline_status["history_messages"].append(status_message)
 
 
 async def _rebuild_single_relationship(
@@ -1157,10 +1222,13 @@ async def _rebuild_single_relationship(
     relationships_vdb: BaseVectorStorage,
     src: str,
     tgt: str,
-    chunk_ids: set[str],
+    chunk_ids: list[str],
     chunk_relationships: dict,
     llm_response_cache: BaseKVStorage,
     global_config: dict[str, str],
+    relation_chunks_storage: BaseKVStorage | None = None,
+    pipeline_status: dict | None = None,
+    pipeline_status_lock=None,
 ) -> None:
     """Rebuild a single relationship from cached extraction results
 
@@ -1173,9 +1241,33 @@ async def _rebuild_single_relationship(
     if not current_relationship:
         return
 
+    # normalized_chunk_ids = merge_source_ids([], chunk_ids)
+    normalized_chunk_ids = chunk_ids
+
+    if relation_chunks_storage is not None and normalized_chunk_ids:
+        storage_key = make_relation_chunk_key(src, tgt)
+        await relation_chunks_storage.upsert(
+            {
+                storage_key: {
+                    "chunk_ids": normalized_chunk_ids,
+                    "count": len(normalized_chunk_ids),
+                }
+            }
+        )
+
+    limit_method = (
+        global_config.get("source_ids_limit_method") or SOURCE_IDS_LIMIT_METHOD_KEEP
+    )
+    limited_chunk_ids = apply_source_ids_limit(
+        normalized_chunk_ids,
+        global_config["max_source_ids_per_relation"],
+        limit_method,
+        identifier=f"`{src}`~`{tgt}`",
+    )
+
     # Collect all relationship data from relevant chunks
     all_relationship_data = []
-    for chunk_id in chunk_ids:
+    for chunk_id in limited_chunk_ids:
         if chunk_id in chunk_relationships:
             # Check both (src, tgt) and (tgt, src) since relationships can be bidirectional
             for edge_key in [(src, tgt), (tgt, src)]:
@@ -1230,6 +1322,13 @@ async def _rebuild_single_relationship(
         # fallback to keep current(unchanged)
         final_description = current_relationship.get("description", "")
 
+    if len(limited_chunk_ids) < len(normalized_chunk_ids):
+        truncation_info = (
+            f"{limit_method}:{len(limited_chunk_ids)}/{len(normalized_chunk_ids)}"
+        )
+    else:
+        truncation_info = ""
+
     # Update relationship in graph storage
     updated_relationship_data = {
         **current_relationship,
@@ -1238,10 +1337,11 @@ async def _rebuild_single_relationship(
         else current_relationship.get("description", ""),
         "keywords": combined_keywords,
         "weight": weight,
-        "source_id": GRAPH_FIELD_SEP.join(chunk_ids),
+        "source_id": GRAPH_FIELD_SEP.join(limited_chunk_ids),
         "file_path": GRAPH_FIELD_SEP.join([fp for fp in file_paths if fp])
         if file_paths
         else current_relationship.get("file_path", "unknown_source"),
+        "truncate": truncation_info,
     }
     await knowledge_graph_inst.upsert_edge(src, tgt, updated_relationship_data)
 
@@ -1287,6 +1387,25 @@ async def _rebuild_single_relationship(
         logger.error(error_msg)
         raise  # Re-raise exception
 
+    # Log rebuild completion with truncation info
+    status_message = f"Rebuild `{src} - {tgt}` from {len(chunk_ids)} chunks"
+    if truncation_info:
+        status_message += f" ({truncation_info})"
+    # Add truncation info from apply_source_ids_limit if truncation occurred
+    if len(limited_chunk_ids) < len(normalized_chunk_ids):
+        truncation_info = (
+            f" ({limit_method}:{len(limited_chunk_ids)}/{len(normalized_chunk_ids)})"
+        )
+        status_message += truncation_info
+
+    logger.info(status_message)
+
+    # Update pipeline status
+    if pipeline_status is not None and pipeline_status_lock is not None:
+        async with pipeline_status_lock:
+            pipeline_status["latest_message"] = status_message
+            pipeline_status["history_messages"].append(status_message)
+
 
 async def _merge_nodes_then_upsert(
     entity_name: str,
@@ -1296,6 +1415,7 @@ async def _merge_nodes_then_upsert(
     pipeline_status: dict = None,
     pipeline_status_lock=None,
     llm_response_cache: BaseKVStorage | None = None,
+    entity_chunks_storage: BaseKVStorage | None = None,
 ):
     """Get existing nodes from knowledge graph use name,if exists, merge data, else create, then upsert."""
     already_entity_types = []
@@ -1318,10 +1438,78 @@ async def _merge_nodes_then_upsert(
         reverse=True,
     )[0][0]  # Get the entity type with the highest count
 
+    original_nodes_count = len(nodes_data)
+
+    new_source_ids = [dp["source_id"] for dp in nodes_data if dp.get("source_id")]
+
+    existing_full_source_ids = []
+    if entity_chunks_storage is not None:
+        stored_chunks = await entity_chunks_storage.get_by_id(entity_name)
+        if stored_chunks and isinstance(stored_chunks, dict):
+            existing_full_source_ids = [
+                chunk_id for chunk_id in stored_chunks.get("chunk_ids", []) if chunk_id
+            ]
+
+    if not existing_full_source_ids:
+        existing_full_source_ids = [
+            chunk_id for chunk_id in already_source_ids if chunk_id
+        ]
+
+    full_source_ids = merge_source_ids(existing_full_source_ids, new_source_ids)
+
+    if entity_chunks_storage is not None and full_source_ids:
+        await entity_chunks_storage.upsert(
+            {
+                entity_name: {
+                    "chunk_ids": full_source_ids,
+                    "count": len(full_source_ids),
+                }
+            }
+        )
+
+    limit_method = (
+        global_config.get("source_ids_limit_method") or SOURCE_IDS_LIMIT_METHOD_KEEP
+    )
+    source_ids = apply_source_ids_limit(
+        full_source_ids,
+        global_config["max_source_ids_per_entity"],
+        limit_method,
+        identifier=f"`{entity_name}`",
+    )
+
+    # Only apply filtering in IGNORE_NEW mode
+    if limit_method == SOURCE_IDS_LIMIT_METHOD_KEEP:
+        allowed_source_ids = set(source_ids)
+        filtered_nodes = []
+        for dp in nodes_data:
+            source_id = dp.get("source_id")
+            # Skip descriptions sourced from chunks dropped by the IGNORE_NEW cap
+            if (
+                source_id
+                and source_id not in allowed_source_ids
+                and source_id not in existing_full_source_ids
+            ):
+                continue
+            filtered_nodes.append(dp)
+        nodes_data = filtered_nodes
+    else:
+        # In FIFO mode, keep all node descriptions - truncation happens at source_ids level only
+        nodes_data = list(nodes_data)
+
+    max_source_limit = global_config["max_source_ids_per_entity"]
+    skip_summary_due_to_limit = (
+        limit_method == SOURCE_IDS_LIMIT_METHOD_KEEP
+        and len(existing_full_source_ids) >= max_source_limit
+        and not nodes_data
+        and already_description
+    )
+
     # Deduplicate by description, keeping first occurrence
     unique_nodes = {}
     for dp in nodes_data:
-        desc = dp["description"]
+        desc = dp.get("description")
+        if not desc:
+            continue
         if desc not in unique_nodes:
             unique_nodes[desc] = dp
 
@@ -1332,17 +1520,31 @@ async def _merge_nodes_then_upsert(
     )
     sorted_descriptions = [dp["description"] for dp in sorted_nodes]
 
+    truncation_info = ""
+    dd_message = ""
+
     # Combine already_description with sorted new sorted descriptions
     description_list = already_description + sorted_descriptions
+    deduplicated_num = original_nodes_count - len(sorted_descriptions)
+    if deduplicated_num > 0:
+        dd_message = f"dd:{deduplicated_num}"
 
     num_fragment = len(description_list)
     already_fragment = len(already_description)
-    deduplicated_num = already_fragment + len(nodes_data) - num_fragment
+    if skip_summary_due_to_limit:
-    if deduplicated_num > 0:
+        description = (
-        dd_message = f"(dd:{deduplicated_num})"
+            already_node.get("description", "(no description)")
-    else:
+            if already_node
-        dd_message = ""
+            else "(no description)"
-    if num_fragment > 0:
+        )
+        llm_was_used = False
+        status_message = f"Skip merge for `{entity_name}`: IGNORE_NEW limit reached"
+        logger.debug(status_message)
+        if pipeline_status is not None and pipeline_status_lock is not None:
+            async with pipeline_status_lock:
+                pipeline_status["latest_message"] = status_message
+                pipeline_status["history_messages"].append(status_message)
+    elif num_fragment > 0:
         # Get summary and LLM usage status
         description, llm_was_used = await _handle_entity_relation_summary(
             "Entity",
@@ -1355,9 +1557,16 @@ async def _merge_nodes_then_upsert(
 
         # Log based on actual LLM usage
         if llm_was_used:
-            status_message = f"LLMmrg: `{entity_name}` | {already_fragment}+{num_fragment - already_fragment}{dd_message}"
+            status_message = f"LLMmrg: `{entity_name}` | {already_fragment}+{num_fragment - already_fragment}"
         else:
-            status_message = f"Merged: `{entity_name}` | {already_fragment}+{num_fragment - already_fragment}{dd_message}"
+            status_message = f"Merged: `{entity_name}` | {already_fragment}+{num_fragment - already_fragment}"
+
+        # Add truncation info from apply_source_ids_limit if truncation occurred
+        if len(source_ids) < len(full_source_ids):
+            truncation_info = f"{limit_method}:{len(source_ids)}/{len(full_source_ids)}"
+
+        if dd_message or truncation_info:
+            status_message += f"({','.join([truncation_info, dd_message])})"
 
         if already_fragment > 0 or llm_was_used:
             logger.info(status_message)
@@ -1372,9 +1581,6 @@ async def _merge_nodes_then_upsert(
         logger.error(f"Entity {entity_name} has no description")
         description = "(no description)"
 
-    merged_source_ids: set = set([dp["source_id"] for dp in nodes_data] + already_source_ids)
-
-    source_ids = truncate_entity_source_id(merged_source_ids, entity_name, global_config)
     source_id = GRAPH_FIELD_SEP.join(source_ids)
 
     file_path = build_file_path(already_file_paths, nodes_data, entity_name)
@@ -1386,6 +1592,7 @@ async def _merge_nodes_then_upsert(
         source_id=source_id,
         file_path=file_path,
         created_at=int(time.time()),
+        truncate=truncation_info,
     )
     await knowledge_graph_inst.upsert_node(
         entity_name,
@@ -1405,6 +1612,7 @@ async def _merge_edges_then_upsert(
     pipeline_status_lock=None,
     llm_response_cache: BaseKVStorage | None = None,
     added_entities: list = None,  # New parameter to track entities added during edge processing
+    relation_chunks_storage: BaseKVStorage | None = None,
 ):
     if src_id == tgt_id:
         return None
@@ -1448,16 +1656,84 @@ async def _merge_edges_then_upsert(
                     )
                 )
 
+    original_edges_count = len(edges_data)
+
+    new_source_ids = [dp["source_id"] for dp in edges_data if dp.get("source_id")]
+
+    storage_key = make_relation_chunk_key(src_id, tgt_id)
+    existing_full_source_ids = []
+    if relation_chunks_storage is not None:
+        stored_chunks = await relation_chunks_storage.get_by_id(storage_key)
+        if stored_chunks and isinstance(stored_chunks, dict):
+            existing_full_source_ids = [
+                chunk_id for chunk_id in stored_chunks.get("chunk_ids", []) if chunk_id
+            ]
+
+    if not existing_full_source_ids:
+        existing_full_source_ids = [
+            chunk_id for chunk_id in already_source_ids if chunk_id
+        ]
+
+    full_source_ids = merge_source_ids(existing_full_source_ids, new_source_ids)
+
+    if relation_chunks_storage is not None and full_source_ids:
+        await relation_chunks_storage.upsert(
+            {
+                storage_key: {
+                    "chunk_ids": full_source_ids,
+                    "count": len(full_source_ids),
+                }
+            }
+        )
+
+    source_ids = apply_source_ids_limit(
+        full_source_ids,
+        global_config["max_source_ids_per_relation"],
+        global_config.get("source_ids_limit_method"),
+        identifier=f"`{src_id}`~`{tgt_id}`",
+    )
+    limit_method = (
+        global_config.get("source_ids_limit_method") or SOURCE_IDS_LIMIT_METHOD_KEEP
+    )
+
+    # Only apply filtering in IGNORE_NEW mode
+    if limit_method == SOURCE_IDS_LIMIT_METHOD_KEEP:
+        allowed_source_ids = set(source_ids)
+        filtered_edges = []
+        for dp in edges_data:
+            source_id = dp.get("source_id")
+            # Skip relationship fragments sourced from chunks dropped by the IGNORE_NEW cap
+            if (
+                source_id
+                and source_id not in allowed_source_ids
+                and source_id not in existing_full_source_ids
+            ):
+                continue
+            filtered_edges.append(dp)
+        edges_data = filtered_edges
+    else:
+        # In FIFO mode, keep all edge descriptions - truncation happens at source_ids level only
+        edges_data = list(edges_data)
+
+    max_source_limit = global_config["max_source_ids_per_relation"]
+    skip_summary_due_to_limit = (
+        limit_method == SOURCE_IDS_LIMIT_METHOD_KEEP
+        and len(existing_full_source_ids) >= max_source_limit
+        and not edges_data
+        and already_description
+    )
+
     # Process edges_data with None checks
     weight = sum([dp["weight"] for dp in edges_data] + already_weights)
 
     # Deduplicate by description, keeping first occurrence
     unique_edges = {}
     for dp in edges_data:
-        if dp.get("description"):
+        description_value = dp.get("description")
-            desc = dp["description"]
+        if not description_value:
-            if desc not in unique_edges:
+            continue
-                unique_edges[desc] = dp
+        if description_value not in unique_edges:
+            unique_edges[description_value] = dp
 
     # Sort description by timestamp, then by description length (largest to smallest) when timestamps are the same
     sorted_edges = sorted(
@@ -1466,17 +1742,34 @@ async def _merge_edges_then_upsert(
     )
     sorted_descriptions = [dp["description"] for dp in sorted_edges]
 
+    truncation_info = ""
+    dd_message = ""
+
     # Combine already_description with sorted new descriptions
     description_list = already_description + sorted_descriptions
+    deduplicated_num = original_edges_count - len(sorted_descriptions)
+    if deduplicated_num > 0:
+        dd_message = f"dd:{deduplicated_num}"
 
     num_fragment = len(description_list)
     already_fragment = len(already_description)
-    deduplicated_num = already_fragment + len(edges_data) - num_fragment
+
-    if deduplicated_num > 0:
+    if skip_summary_due_to_limit:
-        dd_message = f"(dd:{deduplicated_num})"
+        description = (
-    else:
+            already_edge.get("description", "(no description)")
-        dd_message = ""
+            if already_edge
-    if num_fragment > 0:
+            else "(no description)"
+        )
+        llm_was_used = False
+        status_message = (
+            f"Skip merge for `{src_id}`~`{tgt_id}`: IGNORE_NEW limit reached"
+        )
+        logger.debug(status_message)
+        if pipeline_status is not None and pipeline_status_lock is not None:
+            async with pipeline_status_lock:
+                pipeline_status["latest_message"] = status_message
+                pipeline_status["history_messages"].append(status_message)
+    elif num_fragment > 0:
         # Get summary and LLM usage status
         description, llm_was_used = await _handle_entity_relation_summary(
             "Relation",
@@ -1489,9 +1782,16 @@ async def _merge_edges_then_upsert(
 
         # Log based on actual LLM usage
         if llm_was_used:
-            status_message = f"LLMmrg: `{src_id}`~`{tgt_id}` | {already_fragment}+{num_fragment - already_fragment}{dd_message}"
+            status_message = f"LLMmrg: `{src_id}`~`{tgt_id}` | {already_fragment}+{num_fragment - already_fragment}"
         else:
-            status_message = f"Merged: `{src_id}`~`{tgt_id}` | {already_fragment}+{num_fragment - already_fragment}{dd_message}"
+            status_message = f"Merged: `{src_id}`~`{tgt_id}` | {already_fragment}+{num_fragment - already_fragment}"
+
+        # Add truncation info from apply_source_ids_limit if truncation occurred
+        if len(source_ids) < len(full_source_ids):
+            truncation_info = f"{limit_method}:{len(source_ids)}/{len(full_source_ids)}"
+
+        if dd_message or truncation_info:
+            status_message += f"({','.join([truncation_info, dd_message])})"
 
         if already_fragment > 0 or llm_was_used:
             logger.info(status_message)
@@ -1521,12 +1821,7 @@ async def _merge_edges_then_upsert(
     # Join all unique keywords with commas
     keywords = ",".join(sorted(all_keywords))
 
-    source_id = GRAPH_FIELD_SEP.join(
+    source_id = GRAPH_FIELD_SEP.join(source_ids)
-        set(
-            [dp["source_id"] for dp in edges_data if dp.get("source_id")]
-            + already_source_ids
-        )
-    )
     file_path = build_file_path(already_file_paths, edges_data, f"{src_id}-{tgt_id}")
 
     for need_insert_id in [src_id, tgt_id]:
@@ -1538,6 +1833,7 @@ async def _merge_edges_then_upsert(
                 "entity_type": "UNKNOWN",
                 "file_path": file_path,
                 "created_at": int(time.time()),
+                "truncate": "",
             }
             await knowledge_graph_inst.upsert_node(need_insert_id, node_data=node_data)
 
@@ -1563,6 +1859,7 @@ async def _merge_edges_then_upsert(
             source_id=source_id,
             file_path=file_path,
             created_at=int(time.time()),
+            truncate=truncation_info,
         ),
     )
 
@@ -1574,6 +1871,7 @@ async def _merge_edges_then_upsert(
         source_id=source_id,
         file_path=file_path,
         created_at=int(time.time()),
+        truncate=truncation_info,
     )
 
     return edge_data
@@ -1591,6 +1889,8 @@ async def merge_nodes_and_edges(
     pipeline_status: dict = None,
     pipeline_status_lock=None,
     llm_response_cache: BaseKVStorage | None = None,
+    entity_chunks_storage: BaseKVStorage | None = None,
+    relation_chunks_storage: BaseKVStorage | None = None,
     current_file_number: int = 0,
     total_files: int = 0,
     file_path: str = "unknown_source",
@@ -1614,6 +1914,8 @@ async def merge_nodes_and_edges(
         pipeline_status: Pipeline status dictionary
         pipeline_status_lock: Lock for pipeline status
         llm_response_cache: LLM response cache
+        entity_chunks_storage: Storage tracking full chunk lists per entity
+        relation_chunks_storage: Storage tracking full chunk lists per relation
         current_file_number: Current file number for logging
         total_files: Total files for logging
         file_path: File path for logging
@@ -1671,6 +1973,7 @@ async def merge_nodes_and_edges(
                         pipeline_status,
                         pipeline_status_lock,
                         llm_response_cache,
+                        entity_chunks_storage,
                     )
 
                     # Vector database operation (equally critical, must succeed)
@@ -1689,7 +1992,6 @@ async def merge_nodes_and_edges(
                             }
                         }
 
-
                         logger.debug(f"Inserting {entity_name} in Graph")
                         # Use safe operation wrapper - VDB failure must throw exception
                         await safe_vdb_operation_with_exception(
@@ -1804,6 +2106,7 @@ async def merge_nodes_and_edges(
                         pipeline_status_lock,
                         llm_response_cache,
                         added_entities,  # Pass list to collect added entities
+                        relation_chunks_storage,
                     )
 
                     if edge_data is None:

lightrag/utils.py

@@ -15,7 +15,17 @@ from dataclasses import dataclass
 from datetime import datetime
 from functools import wraps
 from hashlib import md5
-from typing import Any, Protocol, Callable, TYPE_CHECKING, List, Optional
+from typing import (
+    Any,
+    Protocol,
+    Callable,
+    TYPE_CHECKING,
+    List,
+    Optional,
+    Iterable,
+    Sequence,
+    Collection,
+)
 import numpy as np
 from dotenv import load_dotenv
 
@@ -26,6 +36,9 @@ from lightrag.constants import (
     GRAPH_FIELD_SEP,
     DEFAULT_MAX_TOTAL_TOKENS,
     DEFAULT_MAX_FILE_PATH_LENGTH,
+    DEFAULT_SOURCE_IDS_LIMIT_METHOD,
+    VALID_SOURCE_IDS_LIMIT_METHODS,
+    SOURCE_IDS_LIMIT_METHOD_FIFO,
 )
 
 # Initialize logger with basic configuration
@@ -2464,24 +2477,112 @@ async def process_chunks_unified(
 
     return final_chunks
 
-def truncate_entity_source_id(chunk_ids: set, entity_name: str, global_config: dict) -> set:
-    """Limit chunk_ids, for entities that appear a HUGE no of times (To not break VDB hard upper limits)"""
-    already_len: int = len(chunk_ids)
 
-    max_chunk_ids_per_entity = global_config["max_source_ids_per_entity"]
+def normalize_source_ids_limit_method(method: str | None) -> str:
+    """Normalize the source ID limiting strategy and fall back to default when invalid."""
 
-    if already_len <= max_chunk_ids_per_entity:
+    if not method:
-        return chunk_ids
+        return DEFAULT_SOURCE_IDS_LIMIT_METHOD
 
+    normalized = method.upper()
+    if normalized not in VALID_SOURCE_IDS_LIMIT_METHODS:
         logger.warning(
-        f"Source Ids already exceeds {max_chunk_ids_per_entity } for {entity_name}, "
+            "Unknown SOURCE_IDS_LIMIT_METHOD '%s', falling back to %s",
-        f"current size: {already_len}, truncating..."
+            method,
+            DEFAULT_SOURCE_IDS_LIMIT_METHOD,
+        )
+        return DEFAULT_SOURCE_IDS_LIMIT_METHOD
+
+    return normalized
+
+
+def merge_source_ids(
+    existing_ids: Iterable[str] | None, new_ids: Iterable[str] | None
+) -> list[str]:
+    """Merge two iterables of source IDs while preserving order and removing duplicates."""
+
+    merged: list[str] = []
+    seen: set[str] = set()
+
+    for sequence in (existing_ids, new_ids):
+        if not sequence:
+            continue
+        for source_id in sequence:
+            if not source_id:
+                continue
+            if source_id not in seen:
+                seen.add(source_id)
+                merged.append(source_id)
+
+    return merged
+
+
+def apply_source_ids_limit(
+    source_ids: Sequence[str],
+    limit: int,
+    method: str,
+    *,
+    identifier: str | None = None,
+) -> list[str]:
+    """Apply a limit strategy to a sequence of source IDs."""
+
+    if limit <= 0:
+        return []
+
+    source_ids_list = list(source_ids)
+    if len(source_ids_list) <= limit:
+        return source_ids_list
+
+    normalized_method = normalize_source_ids_limit_method(method)
+
+    if normalized_method == SOURCE_IDS_LIMIT_METHOD_FIFO:
+        truncated = source_ids_list[-limit:]
+    else:  # IGNORE_NEW
+        truncated = source_ids_list[:limit]
+
+    if identifier and len(truncated) < len(source_ids_list):
+        logger.debug(
+            "Source_id truncated: %s | %s keeping %s of %s entries",
+            identifier,
+            normalized_method,
+            len(truncated),
+            len(source_ids_list),
         )
 
-    truncated_chunk_ids = set(list(chunk_ids)[0:max_chunk_ids_per_entity ])
+    return truncated
-    return truncated_chunk_ids
 
 
+def subtract_source_ids(
+    source_ids: Iterable[str],
+    ids_to_remove: Collection[str],
+) -> list[str]:
+    """Remove a collection of IDs from an ordered iterable while preserving order."""
+
+    removal_set = set(ids_to_remove)
+    if not removal_set:
+        return [source_id for source_id in source_ids if source_id]
+
+    return [
+        source_id
+        for source_id in source_ids
+        if source_id and source_id not in removal_set
+    ]
+
+
+def make_relation_chunk_key(src: str, tgt: str) -> str:
+    """Create a deterministic storage key for relation chunk tracking."""
+
+    return GRAPH_FIELD_SEP.join(sorted((src, tgt)))
+
+
+def parse_relation_chunk_key(key: str) -> tuple[str, str]:
+    """Parse a relation chunk storage key back into its entity pair."""
+
+    parts = key.split(GRAPH_FIELD_SEP)
+    if len(parts) != 2:
+        raise ValueError(f"Invalid relation chunk key: {key}")
+    return parts[0], parts[1]
+
 
 def build_file_path(already_file_paths, data_list, target):
     """Build file path string with UTF-8 byte length limit and deduplication