LightRAG/lightrag/utils_graph.py
yangdx 38559373b3 Fix entity merging to include target entity relationships
* Include target entity in collection
* Merge all relevant relationships
* Prevent relationship loss
* Fix merge completeness
2025-10-26 23:13:50 +08:00

1474 lines
60 KiB
Python

from __future__ import annotations
import time
import asyncio
from typing import Any, cast
from .base import DeletionResult
from .kg.shared_storage import get_graph_db_lock
from .constants import GRAPH_FIELD_SEP
from .utils import compute_mdhash_id, logger
from .base import StorageNameSpace
async def _persist_graph_updates(
entities_vdb=None,
relationships_vdb=None,
chunk_entity_relation_graph=None,
entity_chunks_storage=None,
relation_chunks_storage=None,
) -> None:
"""Unified callback to persist updates after graph operations.
Ensures all relevant storage instances are properly persisted after
operations like delete, edit, create, or merge.
Args:
entities_vdb: Entity vector database storage (optional)
relationships_vdb: Relationship vector database storage (optional)
chunk_entity_relation_graph: Graph storage instance (optional)
entity_chunks_storage: Entity-chunk tracking storage (optional)
relation_chunks_storage: Relation-chunk tracking storage (optional)
"""
storages = []
# Collect all non-None storage instances
if entities_vdb is not None:
storages.append(entities_vdb)
if relationships_vdb is not None:
storages.append(relationships_vdb)
if chunk_entity_relation_graph is not None:
storages.append(chunk_entity_relation_graph)
if entity_chunks_storage is not None:
storages.append(entity_chunks_storage)
if relation_chunks_storage is not None:
storages.append(relation_chunks_storage)
# Persist all storage instances in parallel
if storages:
await asyncio.gather(
*[
cast(StorageNameSpace, storage_inst).index_done_callback()
for storage_inst in storages # type: ignore
]
)
async def adelete_by_entity(
chunk_entity_relation_graph,
entities_vdb,
relationships_vdb,
entity_name: str,
entity_chunks_storage=None,
relation_chunks_storage=None,
) -> DeletionResult:
"""Asynchronously delete an entity and all its relationships.
Also cleans up entity_chunks_storage and relation_chunks_storage to remove chunk tracking.
Args:
chunk_entity_relation_graph: Graph storage instance
entities_vdb: Vector database storage for entities
relationships_vdb: Vector database storage for relationships
entity_name: Name of the entity to delete
entity_chunks_storage: Optional KV storage for tracking chunks that reference this entity
relation_chunks_storage: Optional KV storage for tracking chunks that reference relations
"""
graph_db_lock = get_graph_db_lock(enable_logging=False)
# Use graph database lock to ensure atomic graph and vector db operations
async with graph_db_lock:
try:
# Check if the entity exists
if not await chunk_entity_relation_graph.has_node(entity_name):
logger.warning(f"Entity '{entity_name}' not found.")
return DeletionResult(
status="not_found",
doc_id=entity_name,
message=f"Entity '{entity_name}' not found.",
status_code=404,
)
# Retrieve related relationships before deleting the node
edges = await chunk_entity_relation_graph.get_node_edges(entity_name)
related_relations_count = len(edges) if edges else 0
# Clean up chunk tracking storages before deletion
if entity_chunks_storage is not None:
# Delete entity's entry from entity_chunks_storage
await entity_chunks_storage.delete([entity_name])
logger.info(
f"Entity Delete: removed chunk tracking for `{entity_name}`"
)
if relation_chunks_storage is not None and edges:
# Delete all related relationships from relation_chunks_storage
from .utils import make_relation_chunk_key
relation_keys_to_delete = []
for src, tgt in edges:
# Normalize entity order for consistent key generation
normalized_src, normalized_tgt = sorted([src, tgt])
storage_key = make_relation_chunk_key(
normalized_src, normalized_tgt
)
relation_keys_to_delete.append(storage_key)
if relation_keys_to_delete:
await relation_chunks_storage.delete(relation_keys_to_delete)
logger.info(
f"Entity Delete: removed chunk tracking for {len(relation_keys_to_delete)} relations"
)
await entities_vdb.delete_entity(entity_name)
await relationships_vdb.delete_entity_relation(entity_name)
await chunk_entity_relation_graph.delete_node(entity_name)
message = f"Entity Delete: remove '{entity_name}' and its {related_relations_count} relations"
logger.info(message)
await _persist_graph_updates(
entities_vdb=entities_vdb,
relationships_vdb=relationships_vdb,
chunk_entity_relation_graph=chunk_entity_relation_graph,
entity_chunks_storage=entity_chunks_storage,
relation_chunks_storage=relation_chunks_storage,
)
return DeletionResult(
status="success",
doc_id=entity_name,
message=message,
status_code=200,
)
except Exception as e:
error_message = f"Error while deleting entity '{entity_name}': {e}"
logger.error(error_message)
return DeletionResult(
status="fail",
doc_id=entity_name,
message=error_message,
status_code=500,
)
async def adelete_by_relation(
chunk_entity_relation_graph,
relationships_vdb,
source_entity: str,
target_entity: str,
relation_chunks_storage=None,
) -> DeletionResult:
"""Asynchronously delete a relation between two entities.
Also cleans up relation_chunks_storage to remove chunk tracking.
Args:
chunk_entity_relation_graph: Graph storage instance
relationships_vdb: Vector database storage for relationships
source_entity: Name of the source entity
target_entity: Name of the target entity
relation_chunks_storage: Optional KV storage for tracking chunks that reference this relation
"""
relation_str = f"{source_entity} -> {target_entity}"
graph_db_lock = get_graph_db_lock(enable_logging=False)
# Use graph database lock to ensure atomic graph and vector db operations
async with graph_db_lock:
try:
# Normalize entity order for undirected graph (ensures consistent key generation)
if source_entity > target_entity:
source_entity, target_entity = target_entity, source_entity
# Check if the relation exists
edge_exists = await chunk_entity_relation_graph.has_edge(
source_entity, target_entity
)
if not edge_exists:
message = f"Relation from '{source_entity}' to '{target_entity}' does not exist"
logger.warning(message)
return DeletionResult(
status="not_found",
doc_id=relation_str,
message=message,
status_code=404,
)
# Clean up chunk tracking storage before deletion
if relation_chunks_storage is not None:
from .utils import make_relation_chunk_key
# Normalize entity order for consistent key generation
normalized_src, normalized_tgt = sorted([source_entity, target_entity])
storage_key = make_relation_chunk_key(normalized_src, normalized_tgt)
await relation_chunks_storage.delete([storage_key])
logger.info(
f"Relation Delete: removed chunk tracking for `{source_entity}`~`{target_entity}`"
)
# Delete relation from vector database
rel_ids_to_delete = [
compute_mdhash_id(source_entity + target_entity, prefix="rel-"),
compute_mdhash_id(target_entity + source_entity, prefix="rel-"),
]
await relationships_vdb.delete(rel_ids_to_delete)
# Delete relation from knowledge graph
await chunk_entity_relation_graph.remove_edges(
[(source_entity, target_entity)]
)
message = f"Relation Delete: `{source_entity}`~`{target_entity}` deleted successfully"
logger.info(message)
await _persist_graph_updates(
relationships_vdb=relationships_vdb,
chunk_entity_relation_graph=chunk_entity_relation_graph,
relation_chunks_storage=relation_chunks_storage,
)
return DeletionResult(
status="success",
doc_id=relation_str,
message=message,
status_code=200,
)
except Exception as e:
error_message = f"Error while deleting relation from '{source_entity}' to '{target_entity}': {e}"
logger.error(error_message)
return DeletionResult(
status="fail",
doc_id=relation_str,
message=error_message,
status_code=500,
)
async def aedit_entity(
chunk_entity_relation_graph,
entities_vdb,
relationships_vdb,
entity_name: str,
updated_data: dict[str, str],
allow_rename: bool = True,
entity_chunks_storage=None,
relation_chunks_storage=None,
) -> dict[str, Any]:
"""Asynchronously edit entity information.
Updates entity information in the knowledge graph and re-embeds the entity in the vector database.
Also synchronizes entity_chunks_storage and relation_chunks_storage to track chunk references.
Args:
chunk_entity_relation_graph: Graph storage instance
entities_vdb: Vector database storage for entities
relationships_vdb: Vector database storage for relationships
entity_name: Name of the entity to edit
updated_data: Dictionary containing updated attributes, e.g. {"description": "new description", "entity_type": "new type"}
allow_rename: Whether to allow entity renaming, defaults to True
entity_chunks_storage: Optional KV storage for tracking chunks that reference this entity
relation_chunks_storage: Optional KV storage for tracking chunks that reference relations
Returns:
Dictionary containing updated entity information
"""
graph_db_lock = get_graph_db_lock(enable_logging=False)
# Use graph database lock to ensure atomic graph and vector db operations
async with graph_db_lock:
try:
# Save original entity name for chunk tracking updates
original_entity_name = entity_name
# 1. Get current entity information
node_exists = await chunk_entity_relation_graph.has_node(entity_name)
if not node_exists:
raise ValueError(f"Entity '{entity_name}' does not exist")
node_data = await chunk_entity_relation_graph.get_node(entity_name)
# Check if entity is being renamed
new_entity_name = updated_data.get("entity_name", entity_name)
is_renaming = new_entity_name != entity_name
# If renaming, check if new name already exists
if is_renaming:
if not allow_rename:
raise ValueError(
"Entity renaming is not allowed. Set allow_rename=True to enable this feature"
)
existing_node = await chunk_entity_relation_graph.has_node(
new_entity_name
)
if existing_node:
raise ValueError(
f"Entity name '{new_entity_name}' already exists, cannot rename"
)
# 2. Update entity information in the graph
new_node_data = {**node_data, **updated_data}
new_node_data["entity_id"] = new_entity_name
if "entity_name" in new_node_data:
del new_node_data[
"entity_name"
] # Node data should not contain entity_name field
# If renaming entity
if is_renaming:
logger.info(
f"Entity Edit: renaming `{entity_name}` to `{new_entity_name}`"
)
# Create new entity
await chunk_entity_relation_graph.upsert_node(
new_entity_name, new_node_data
)
# Store relationships that need to be updated
relations_to_update = []
relations_to_delete = []
# Get all edges related to the original entity
edges = await chunk_entity_relation_graph.get_node_edges(entity_name)
if edges:
# Recreate edges for the new entity
for source, target in edges:
edge_data = await chunk_entity_relation_graph.get_edge(
source, target
)
if edge_data:
relations_to_delete.append(
compute_mdhash_id(source + target, prefix="rel-")
)
relations_to_delete.append(
compute_mdhash_id(target + source, prefix="rel-")
)
if source == entity_name:
await chunk_entity_relation_graph.upsert_edge(
new_entity_name, target, edge_data
)
relations_to_update.append(
(new_entity_name, target, edge_data)
)
else: # target == entity_name
await chunk_entity_relation_graph.upsert_edge(
source, new_entity_name, edge_data
)
relations_to_update.append(
(source, new_entity_name, edge_data)
)
# Delete old entity
await chunk_entity_relation_graph.delete_node(entity_name)
# Delete old entity record from vector database
old_entity_id = compute_mdhash_id(entity_name, prefix="ent-")
await entities_vdb.delete([old_entity_id])
# Delete old relation records from vector database
await relationships_vdb.delete(relations_to_delete)
# Update relationship vector representations
for src, tgt, edge_data in relations_to_update:
# Normalize entity order for consistent vector ID generation
normalized_src, normalized_tgt = sorted([src, tgt])
description = edge_data.get("description", "")
keywords = edge_data.get("keywords", "")
source_id = edge_data.get("source_id", "")
weight = float(edge_data.get("weight", 1.0))
# Create content using normalized order
content = (
f"{normalized_src}\t{normalized_tgt}\n{keywords}\n{description}"
)
# Calculate relationship ID using normalized order
relation_id = compute_mdhash_id(
normalized_src + normalized_tgt, prefix="rel-"
)
# Prepare data for vector database update
relation_data = {
relation_id: {
"content": content,
"src_id": normalized_src,
"tgt_id": normalized_tgt,
"source_id": source_id,
"description": description,
"keywords": keywords,
"weight": weight,
}
}
# Update vector database
await relationships_vdb.upsert(relation_data)
# Update working entity name to new name
entity_name = new_entity_name
else:
# If not renaming, directly update node data
await chunk_entity_relation_graph.upsert_node(
entity_name, new_node_data
)
# 3. Recalculate entity's vector representation and update vector database
description = new_node_data.get("description", "")
source_id = new_node_data.get("source_id", "")
entity_type = new_node_data.get("entity_type", "")
content = entity_name + "\n" + description
# Calculate entity ID
entity_id = compute_mdhash_id(entity_name, prefix="ent-")
# Prepare data for vector database update
entity_data = {
entity_id: {
"content": content,
"entity_name": entity_name,
"source_id": source_id,
"description": description,
"entity_type": entity_type,
}
}
# Update vector database
await entities_vdb.upsert(entity_data)
# 4. Update chunk tracking storages
if entity_chunks_storage is not None or relation_chunks_storage is not None:
from .utils import (
make_relation_chunk_key,
compute_incremental_chunk_ids,
)
# 4.1 Handle entity chunk tracking
if entity_chunks_storage is not None:
# Get storage key (use original name for renaming scenario)
storage_key = original_entity_name if is_renaming else entity_name
stored_data = await entity_chunks_storage.get_by_id(storage_key)
has_stored_data = (
stored_data
and isinstance(stored_data, dict)
and stored_data.get("chunk_ids")
)
# Get old and new source_id
old_source_id = node_data.get("source_id", "")
old_chunk_ids = [
cid for cid in old_source_id.split(GRAPH_FIELD_SEP) if cid
]
new_source_id = new_node_data.get("source_id", "")
new_chunk_ids = [
cid for cid in new_source_id.split(GRAPH_FIELD_SEP) if cid
]
source_id_changed = set(new_chunk_ids) != set(old_chunk_ids)
# Update if: source_id changed OR storage has no data
if source_id_changed or not has_stored_data:
# Get existing full chunk_ids from storage
existing_full_chunk_ids = []
if has_stored_data:
existing_full_chunk_ids = [
cid for cid in stored_data.get("chunk_ids", []) if cid
]
# If no stored data exists, use old source_id as baseline
if not existing_full_chunk_ids:
existing_full_chunk_ids = old_chunk_ids.copy()
# Use utility function to compute incremental updates
updated_chunk_ids = compute_incremental_chunk_ids(
existing_full_chunk_ids, old_chunk_ids, new_chunk_ids
)
# Update storage (even if updated_chunk_ids is empty)
if is_renaming:
# Renaming: delete old + create new
await entity_chunks_storage.delete([original_entity_name])
await entity_chunks_storage.upsert(
{
entity_name: {
"chunk_ids": updated_chunk_ids,
"count": len(updated_chunk_ids),
}
}
)
else:
# Non-renaming: direct update
await entity_chunks_storage.upsert(
{
entity_name: {
"chunk_ids": updated_chunk_ids,
"count": len(updated_chunk_ids),
}
}
)
logger.info(
f"Entity Edit: find {len(updated_chunk_ids)} chunks related to `{entity_name}`"
)
# 4.2 Handle relation chunk tracking if entity was renamed
if (
is_renaming
and relation_chunks_storage is not None
and relations_to_update
):
for src, tgt, edge_data in relations_to_update:
# Determine old entity pair (before rename)
old_src = original_entity_name if src == entity_name else src
old_tgt = original_entity_name if tgt == entity_name else tgt
# Normalize entity order for both old and new keys
old_normalized_src, old_normalized_tgt = sorted(
[old_src, old_tgt]
)
new_normalized_src, new_normalized_tgt = sorted([src, tgt])
# Generate storage keys
old_storage_key = make_relation_chunk_key(
old_normalized_src, old_normalized_tgt
)
new_storage_key = make_relation_chunk_key(
new_normalized_src, new_normalized_tgt
)
# If keys are different, we need to move the chunk tracking
if old_storage_key != new_storage_key:
# Get complete chunk IDs from storage first (preserves all existing references)
old_stored_data = await relation_chunks_storage.get_by_id(
old_storage_key
)
relation_chunk_ids = []
if old_stored_data and isinstance(old_stored_data, dict):
# Use complete chunk_ids from storage
relation_chunk_ids = [
cid
for cid in old_stored_data.get("chunk_ids", [])
if cid
]
else:
# Fallback: if storage has no data, use graph's source_id
relation_source_id = edge_data.get("source_id", "")
relation_chunk_ids = [
cid
for cid in relation_source_id.split(GRAPH_FIELD_SEP)
if cid
]
# Delete old relation chunk tracking
await relation_chunks_storage.delete([old_storage_key])
# Create new relation chunk tracking (migrate complete data)
if relation_chunk_ids:
await relation_chunks_storage.upsert(
{
new_storage_key: {
"chunk_ids": relation_chunk_ids,
"count": len(relation_chunk_ids),
}
}
)
logger.info(
f"Entity Edit: migrate {len(relations_to_update)} relations after rename"
)
# 5. Save changes
await _persist_graph_updates(
entities_vdb=entities_vdb,
relationships_vdb=relationships_vdb,
chunk_entity_relation_graph=chunk_entity_relation_graph,
entity_chunks_storage=entity_chunks_storage,
relation_chunks_storage=relation_chunks_storage,
)
logger.info(f"Entity Edit: `{entity_name}` successfully updated")
return await get_entity_info(
chunk_entity_relation_graph,
entities_vdb,
entity_name,
include_vector_data=True,
)
except Exception as e:
logger.error(f"Error while editing entity '{entity_name}': {e}")
raise
async def aedit_relation(
chunk_entity_relation_graph,
entities_vdb,
relationships_vdb,
source_entity: str,
target_entity: str,
updated_data: dict[str, Any],
relation_chunks_storage=None,
) -> dict[str, Any]:
"""Asynchronously edit relation information.
Updates relation (edge) information in the knowledge graph and re-embeds the relation in the vector database.
Also synchronizes the relation_chunks_storage to track which chunks reference this relation.
Args:
chunk_entity_relation_graph: Graph storage instance
entities_vdb: Vector database storage for entities
relationships_vdb: Vector database storage for relationships
source_entity: Name of the source entity
target_entity: Name of the target entity
updated_data: Dictionary containing updated attributes, e.g. {"description": "new description", "keywords": "new keywords"}
relation_chunks_storage: Optional KV storage for tracking chunks that reference this relation
Returns:
Dictionary containing updated relation information
"""
graph_db_lock = get_graph_db_lock(enable_logging=False)
# Use graph database lock to ensure atomic graph and vector db operations
async with graph_db_lock:
try:
# Normalize entity order for undirected graph (ensures consistent key generation)
if source_entity > target_entity:
source_entity, target_entity = target_entity, source_entity
# 1. Get current relation information
edge_exists = await chunk_entity_relation_graph.has_edge(
source_entity, target_entity
)
if not edge_exists:
raise ValueError(
f"Relation from '{source_entity}' to '{target_entity}' does not exist"
)
edge_data = await chunk_entity_relation_graph.get_edge(
source_entity, target_entity
)
# Important: First delete the old relation record from the vector database
# Delete both permutations to handle relationships created before normalization
rel_ids_to_delete = [
compute_mdhash_id(source_entity + target_entity, prefix="rel-"),
compute_mdhash_id(target_entity + source_entity, prefix="rel-"),
]
await relationships_vdb.delete(rel_ids_to_delete)
logger.debug(
f"Relation Delete: delete vdb for `{source_entity}`~`{target_entity}`"
)
# 2. Update relation information in the graph
new_edge_data = {**edge_data, **updated_data}
await chunk_entity_relation_graph.upsert_edge(
source_entity, target_entity, new_edge_data
)
# 3. Recalculate relation's vector representation and update vector database
description = new_edge_data.get("description", "")
keywords = new_edge_data.get("keywords", "")
source_id = new_edge_data.get("source_id", "")
weight = float(new_edge_data.get("weight", 1.0))
# Create content for embedding
content = f"{source_entity}\t{target_entity}\n{keywords}\n{description}"
# Calculate relation ID
relation_id = compute_mdhash_id(
source_entity + target_entity, prefix="rel-"
)
# Prepare data for vector database update
relation_data = {
relation_id: {
"content": content,
"src_id": source_entity,
"tgt_id": target_entity,
"source_id": source_id,
"description": description,
"keywords": keywords,
"weight": weight,
}
}
# Update vector database
await relationships_vdb.upsert(relation_data)
# 4. Update relation_chunks_storage in two scenarios:
# - source_id has changed (edit scenario)
# - relation_chunks_storage has no existing data (migration/initialization scenario)
if relation_chunks_storage is not None:
from .utils import (
make_relation_chunk_key,
compute_incremental_chunk_ids,
)
storage_key = make_relation_chunk_key(source_entity, target_entity)
# Check if storage has existing data
stored_data = await relation_chunks_storage.get_by_id(storage_key)
has_stored_data = (
stored_data
and isinstance(stored_data, dict)
and stored_data.get("chunk_ids")
)
# Get old and new source_id
old_source_id = edge_data.get("source_id", "")
old_chunk_ids = [
cid for cid in old_source_id.split(GRAPH_FIELD_SEP) if cid
]
new_source_id = new_edge_data.get("source_id", "")
new_chunk_ids = [
cid for cid in new_source_id.split(GRAPH_FIELD_SEP) if cid
]
source_id_changed = set(new_chunk_ids) != set(old_chunk_ids)
# Update if: source_id changed OR storage has no data
if source_id_changed or not has_stored_data:
# Get existing full chunk_ids from storage
existing_full_chunk_ids = []
if has_stored_data:
existing_full_chunk_ids = [
cid for cid in stored_data.get("chunk_ids", []) if cid
]
# If no stored data exists, use old source_id as baseline
if not existing_full_chunk_ids:
existing_full_chunk_ids = old_chunk_ids.copy()
# Use utility function to compute incremental updates
updated_chunk_ids = compute_incremental_chunk_ids(
existing_full_chunk_ids, old_chunk_ids, new_chunk_ids
)
# Update storage (Update even if updated_chunk_ids is empty)
await relation_chunks_storage.upsert(
{
storage_key: {
"chunk_ids": updated_chunk_ids,
"count": len(updated_chunk_ids),
}
}
)
logger.info(
f"Relation Delete: update chunk tracking for `{source_entity}`~`{target_entity}`"
)
# 5. Save changes
await _persist_graph_updates(
relationships_vdb=relationships_vdb,
chunk_entity_relation_graph=chunk_entity_relation_graph,
relation_chunks_storage=relation_chunks_storage,
)
logger.info(
f"Relation Delete: `{source_entity}`~`{target_entity}`' successfully updated"
)
return await get_relation_info(
chunk_entity_relation_graph,
relationships_vdb,
source_entity,
target_entity,
include_vector_data=True,
)
except Exception as e:
logger.error(
f"Error while editing relation from '{source_entity}' to '{target_entity}': {e}"
)
raise
async def acreate_entity(
chunk_entity_relation_graph,
entities_vdb,
relationships_vdb,
entity_name: str,
entity_data: dict[str, Any],
entity_chunks_storage=None,
relation_chunks_storage=None,
) -> dict[str, Any]:
"""Asynchronously create a new entity.
Creates a new entity in the knowledge graph and adds it to the vector database.
Also synchronizes entity_chunks_storage to track chunk references.
Args:
chunk_entity_relation_graph: Graph storage instance
entities_vdb: Vector database storage for entities
relationships_vdb: Vector database storage for relationships
entity_name: Name of the new entity
entity_data: Dictionary containing entity attributes, e.g. {"description": "description", "entity_type": "type"}
entity_chunks_storage: Optional KV storage for tracking chunks that reference this entity
relation_chunks_storage: Optional KV storage for tracking chunks that reference relations
Returns:
Dictionary containing created entity information
"""
graph_db_lock = get_graph_db_lock(enable_logging=False)
# Use graph database lock to ensure atomic graph and vector db operations
async with graph_db_lock:
try:
# Check if entity already exists
existing_node = await chunk_entity_relation_graph.has_node(entity_name)
if existing_node:
raise ValueError(f"Entity '{entity_name}' already exists")
# Prepare node data with defaults if missing
node_data = {
"entity_id": entity_name,
"entity_type": entity_data.get("entity_type", "UNKNOWN"),
"description": entity_data.get("description", ""),
"source_id": entity_data.get("source_id", "manual_creation"),
"file_path": entity_data.get("file_path", "manual_creation"),
"created_at": int(time.time()),
}
# Add entity to knowledge graph
await chunk_entity_relation_graph.upsert_node(entity_name, node_data)
# Prepare content for entity
description = node_data.get("description", "")
source_id = node_data.get("source_id", "")
entity_type = node_data.get("entity_type", "")
content = entity_name + "\n" + description
# Calculate entity ID
entity_id = compute_mdhash_id(entity_name, prefix="ent-")
# Prepare data for vector database update
entity_data_for_vdb = {
entity_id: {
"content": content,
"entity_name": entity_name,
"source_id": source_id,
"description": description,
"entity_type": entity_type,
"file_path": entity_data.get("file_path", "manual_creation"),
}
}
# Update vector database
await entities_vdb.upsert(entity_data_for_vdb)
# Update entity_chunks_storage to track chunk references
if entity_chunks_storage is not None:
source_id = node_data.get("source_id", "")
chunk_ids = [cid for cid in source_id.split(GRAPH_FIELD_SEP) if cid]
if chunk_ids:
await entity_chunks_storage.upsert(
{
entity_name: {
"chunk_ids": chunk_ids,
"count": len(chunk_ids),
}
}
)
logger.info(
f"Entity Create: tracked {len(chunk_ids)} chunks for `{entity_name}`"
)
# Save changes
await _persist_graph_updates(
entities_vdb=entities_vdb,
relationships_vdb=relationships_vdb,
chunk_entity_relation_graph=chunk_entity_relation_graph,
entity_chunks_storage=entity_chunks_storage,
relation_chunks_storage=relation_chunks_storage,
)
logger.info(f"Entity Create: '{entity_name}' successfully created")
return await get_entity_info(
chunk_entity_relation_graph,
entities_vdb,
entity_name,
include_vector_data=True,
)
except Exception as e:
logger.error(f"Error while creating entity '{entity_name}': {e}")
raise
async def acreate_relation(
chunk_entity_relation_graph,
entities_vdb,
relationships_vdb,
source_entity: str,
target_entity: str,
relation_data: dict[str, Any],
relation_chunks_storage=None,
) -> dict[str, Any]:
"""Asynchronously create a new relation between entities.
Creates a new relation (edge) in the knowledge graph and adds it to the vector database.
Also synchronizes relation_chunks_storage to track chunk references.
Args:
chunk_entity_relation_graph: Graph storage instance
entities_vdb: Vector database storage for entities
relationships_vdb: Vector database storage for relationships
source_entity: Name of the source entity
target_entity: Name of the target entity
relation_data: Dictionary containing relation attributes, e.g. {"description": "description", "keywords": "keywords"}
relation_chunks_storage: Optional KV storage for tracking chunks that reference this relation
Returns:
Dictionary containing created relation information
"""
graph_db_lock = get_graph_db_lock(enable_logging=False)
# Use graph database lock to ensure atomic graph and vector db operations
async with graph_db_lock:
try:
# Check if both entities exist
source_exists = await chunk_entity_relation_graph.has_node(source_entity)
target_exists = await chunk_entity_relation_graph.has_node(target_entity)
if not source_exists:
raise ValueError(f"Source entity '{source_entity}' does not exist")
if not target_exists:
raise ValueError(f"Target entity '{target_entity}' does not exist")
# Check if relation already exists
existing_edge = await chunk_entity_relation_graph.has_edge(
source_entity, target_entity
)
if existing_edge:
raise ValueError(
f"Relation from '{source_entity}' to '{target_entity}' already exists"
)
# Prepare edge data with defaults if missing
edge_data = {
"description": relation_data.get("description", ""),
"keywords": relation_data.get("keywords", ""),
"source_id": relation_data.get("source_id", "manual_creation"),
"weight": float(relation_data.get("weight", 1.0)),
"file_path": relation_data.get("file_path", "manual_creation"),
"created_at": int(time.time()),
}
# Add relation to knowledge graph
await chunk_entity_relation_graph.upsert_edge(
source_entity, target_entity, edge_data
)
# Normalize entity order for undirected relation vector (ensures consistent key generation)
if source_entity > target_entity:
source_entity, target_entity = target_entity, source_entity
# Prepare content for embedding
description = edge_data.get("description", "")
keywords = edge_data.get("keywords", "")
source_id = edge_data.get("source_id", "")
weight = edge_data.get("weight", 1.0)
# Create content for embedding
content = f"{keywords}\t{source_entity}\n{target_entity}\n{description}"
# Calculate relation ID
relation_id = compute_mdhash_id(
source_entity + target_entity, prefix="rel-"
)
# Prepare data for vector database update
relation_data_for_vdb = {
relation_id: {
"content": content,
"src_id": source_entity,
"tgt_id": target_entity,
"source_id": source_id,
"description": description,
"keywords": keywords,
"weight": weight,
"file_path": relation_data.get("file_path", "manual_creation"),
}
}
# Update vector database
await relationships_vdb.upsert(relation_data_for_vdb)
# Update relation_chunks_storage to track chunk references
if relation_chunks_storage is not None:
from .utils import make_relation_chunk_key
# Normalize entity order for consistent key generation
normalized_src, normalized_tgt = sorted([source_entity, target_entity])
storage_key = make_relation_chunk_key(normalized_src, normalized_tgt)
source_id = edge_data.get("source_id", "")
chunk_ids = [cid for cid in source_id.split(GRAPH_FIELD_SEP) if cid]
if chunk_ids:
await relation_chunks_storage.upsert(
{
storage_key: {
"chunk_ids": chunk_ids,
"count": len(chunk_ids),
}
}
)
logger.info(
f"Relation Create: tracked {len(chunk_ids)} chunks for `{source_entity}`~`{target_entity}`"
)
# Save changes
await _persist_graph_updates(
relationships_vdb=relationships_vdb,
chunk_entity_relation_graph=chunk_entity_relation_graph,
relation_chunks_storage=relation_chunks_storage,
)
logger.info(
f"Relation Create: `{source_entity}`~`{target_entity}` successfully created"
)
return await get_relation_info(
chunk_entity_relation_graph,
relationships_vdb,
source_entity,
target_entity,
include_vector_data=True,
)
except Exception as e:
logger.error(
f"Error while creating relation from '{source_entity}' to '{target_entity}': {e}"
)
raise
async def amerge_entities(
chunk_entity_relation_graph,
entities_vdb,
relationships_vdb,
source_entities: list[str],
target_entity: str,
merge_strategy: dict[str, str] = None,
target_entity_data: dict[str, Any] = None,
) -> dict[str, Any]:
"""Asynchronously merge multiple entities into one entity.
Merges multiple source entities into a target entity, handling all relationships,
and updating both the knowledge graph and vector database.
Args:
chunk_entity_relation_graph: Graph storage instance
entities_vdb: Vector database storage for entities
relationships_vdb: Vector database storage for relationships
source_entities: List of source entity names to merge
target_entity: Name of the target entity after merging
merge_strategy: Merge strategy configuration, e.g. {"description": "concatenate", "entity_type": "keep_first"}
Supported strategies:
- "concatenate": Concatenate all values (for text fields)
- "keep_first": Keep the first non-empty value
- "keep_last": Keep the last non-empty value
- "join_unique": Join all unique values (for fields separated by delimiter)
target_entity_data: Dictionary of specific values to set for the target entity,
overriding any merged values, e.g. {"description": "custom description", "entity_type": "PERSON"}
Returns:
Dictionary containing the merged entity information
"""
graph_db_lock = get_graph_db_lock(enable_logging=False)
# Use graph database lock to ensure atomic graph and vector db operations
async with graph_db_lock:
try:
# Default merge strategy
default_strategy = {
"description": "concatenate",
"entity_type": "keep_first",
"source_id": "join_unique",
}
merge_strategy = (
default_strategy
if merge_strategy is None
else {**default_strategy, **merge_strategy}
)
target_entity_data = (
{} if target_entity_data is None else target_entity_data
)
# 1. Check if all source entities exist
source_entities_data = {}
for entity_name in source_entities:
node_exists = await chunk_entity_relation_graph.has_node(entity_name)
if not node_exists:
raise ValueError(f"Source entity '{entity_name}' does not exist")
node_data = await chunk_entity_relation_graph.get_node(entity_name)
source_entities_data[entity_name] = node_data
# 2. Check if target entity exists and get its data if it does
target_exists = await chunk_entity_relation_graph.has_node(target_entity)
existing_target_entity_data = {}
if target_exists:
existing_target_entity_data = (
await chunk_entity_relation_graph.get_node(target_entity)
)
logger.info(
f"Target entity '{target_entity}' already exists, will merge data"
)
# 3. Merge entity data
merged_entity_data = _merge_entity_attributes(
list(source_entities_data.values())
+ ([existing_target_entity_data] if target_exists else []),
merge_strategy,
)
# Apply any explicitly provided target entity data (overrides merged data)
for key, value in target_entity_data.items():
merged_entity_data[key] = value
# 4. Get all relationships of the source entities and target entity (if exists)
all_relations = []
entities_to_collect = source_entities.copy()
# If target entity exists, also collect its relationships for merging
if target_exists:
entities_to_collect.append(target_entity)
for entity_name in entities_to_collect:
# Get all relationships of the entities
edges = await chunk_entity_relation_graph.get_node_edges(entity_name)
if edges:
for src, tgt in edges:
# Ensure src is the current entity
if src == entity_name:
edge_data = await chunk_entity_relation_graph.get_edge(
src, tgt
)
all_relations.append((src, tgt, edge_data))
# 5. Create or update the target entity
merged_entity_data["entity_id"] = target_entity
if not target_exists:
await chunk_entity_relation_graph.upsert_node(
target_entity, merged_entity_data
)
logger.info(f"Created new target entity '{target_entity}'")
else:
await chunk_entity_relation_graph.upsert_node(
target_entity, merged_entity_data
)
logger.info(f"Updated existing target entity '{target_entity}'")
# 6. Recreate all relationships, pointing to the target entity
relation_updates = {} # Track relationships that need to be merged
relations_to_delete = []
for src, tgt, edge_data in all_relations:
relations_to_delete.append(compute_mdhash_id(src + tgt, prefix="rel-"))
relations_to_delete.append(compute_mdhash_id(tgt + src, prefix="rel-"))
new_src = target_entity if src in source_entities else src
new_tgt = target_entity if tgt in source_entities else tgt
# Skip relationships between source entities to avoid self-loops
if new_src == new_tgt:
logger.info(
f"Skipping relationship between source entities: {src} -> {tgt} to avoid self-loop"
)
continue
# Check if the same relationship already exists
relation_key = f"{new_src}|{new_tgt}"
if relation_key in relation_updates:
# Merge relationship data
existing_data = relation_updates[relation_key]["data"]
merged_relation = _merge_relation_attributes(
[existing_data, edge_data],
{
"description": "concatenate",
"keywords": "join_unique",
"source_id": "join_unique",
"weight": "max",
},
)
relation_updates[relation_key]["data"] = merged_relation
logger.info(
f"Merged duplicate relationship: {new_src} -> {new_tgt}"
)
else:
relation_updates[relation_key] = {
"src": new_src,
"tgt": new_tgt,
"data": edge_data.copy(),
}
# Apply relationship updates
for rel_data in relation_updates.values():
await chunk_entity_relation_graph.upsert_edge(
rel_data["src"], rel_data["tgt"], rel_data["data"]
)
logger.info(
f"Created or updated relationship: {rel_data['src']} -> {rel_data['tgt']}"
)
# Delete relationships records from vector database
await relationships_vdb.delete(relations_to_delete)
logger.info(
f"Deleted {len(relations_to_delete)} relation records for entity from vector database"
)
# 7. Update entity vector representation
description = merged_entity_data.get("description", "")
source_id = merged_entity_data.get("source_id", "")
entity_type = merged_entity_data.get("entity_type", "")
content = target_entity + "\n" + description
entity_id = compute_mdhash_id(target_entity, prefix="ent-")
entity_data_for_vdb = {
entity_id: {
"content": content,
"entity_name": target_entity,
"source_id": source_id,
"description": description,
"entity_type": entity_type,
}
}
await entities_vdb.upsert(entity_data_for_vdb)
# 8. Update relationship vector representations
for rel_data in relation_updates.values():
src = rel_data["src"]
tgt = rel_data["tgt"]
edge_data = rel_data["data"]
# Normalize entity order for consistent vector storage
normalized_src, normalized_tgt = sorted([src, tgt])
description = edge_data.get("description", "")
keywords = edge_data.get("keywords", "")
source_id = edge_data.get("source_id", "")
weight = float(edge_data.get("weight", 1.0))
# Use normalized order for content and relation ID
content = (
f"{keywords}\t{normalized_src}\n{normalized_tgt}\n{description}"
)
relation_id = compute_mdhash_id(
normalized_src + normalized_tgt, prefix="rel-"
)
relation_data_for_vdb = {
relation_id: {
"content": content,
"src_id": normalized_src,
"tgt_id": normalized_tgt,
"source_id": source_id,
"description": description,
"keywords": keywords,
"weight": weight,
}
}
await relationships_vdb.upsert(relation_data_for_vdb)
# 9. Delete source entities
for entity_name in source_entities:
if entity_name == target_entity:
logger.info(
f"Skipping deletion of '{entity_name}' as it's also the target entity"
)
continue
# Delete entity node from knowledge graph
await chunk_entity_relation_graph.delete_node(entity_name)
# Delete entity record from vector database
entity_id = compute_mdhash_id(entity_name, prefix="ent-")
await entities_vdb.delete([entity_id])
logger.info(
f"Deleted source entity '{entity_name}' and its vector embedding from database"
)
# 10. Save changes
await _persist_graph_updates(
entities_vdb=entities_vdb,
relationships_vdb=relationships_vdb,
chunk_entity_relation_graph=chunk_entity_relation_graph,
)
logger.info(
f"Successfully merged {len(source_entities)} entities into '{target_entity}'"
)
return await get_entity_info(
chunk_entity_relation_graph,
entities_vdb,
target_entity,
include_vector_data=True,
)
except Exception as e:
logger.error(f"Error merging entities: {e}")
raise
def _merge_entity_attributes(
entity_data_list: list[dict[str, Any]], merge_strategy: dict[str, str]
) -> dict[str, Any]:
"""Merge attributes from multiple entities.
Args:
entity_data_list: List of dictionaries containing entity data
merge_strategy: Merge strategy for each field
Returns:
Dictionary containing merged entity data
"""
merged_data = {}
# Collect all possible keys
all_keys = set()
for data in entity_data_list:
all_keys.update(data.keys())
# Merge values for each key
for key in all_keys:
# Get all values for this key
values = [data.get(key) for data in entity_data_list if data.get(key)]
if not values:
continue
# Merge values according to strategy
strategy = merge_strategy.get(key, "keep_first")
if strategy == "concatenate":
merged_data[key] = "\n\n".join(values)
elif strategy == "keep_first":
merged_data[key] = values[0]
elif strategy == "keep_last":
merged_data[key] = values[-1]
elif strategy == "join_unique":
# Handle fields separated by GRAPH_FIELD_SEP
unique_items = set()
for value in values:
items = value.split(GRAPH_FIELD_SEP)
unique_items.update(items)
merged_data[key] = GRAPH_FIELD_SEP.join(unique_items)
else:
# Default strategy
merged_data[key] = values[0]
return merged_data
def _merge_relation_attributes(
relation_data_list: list[dict[str, Any]], merge_strategy: dict[str, str]
) -> dict[str, Any]:
"""Merge attributes from multiple relationships.
Args:
relation_data_list: List of dictionaries containing relationship data
merge_strategy: Merge strategy for each field
Returns:
Dictionary containing merged relationship data
"""
merged_data = {}
# Collect all possible keys
all_keys = set()
for data in relation_data_list:
all_keys.update(data.keys())
# Merge values for each key
for key in all_keys:
# Get all values for this key
values = [
data.get(key) for data in relation_data_list if data.get(key) is not None
]
if not values:
continue
# Merge values according to strategy
strategy = merge_strategy.get(key, "keep_first")
if strategy == "concatenate":
merged_data[key] = "\n\n".join(str(v) for v in values)
elif strategy == "keep_first":
merged_data[key] = values[0]
elif strategy == "keep_last":
merged_data[key] = values[-1]
elif strategy == "join_unique":
# Handle fields separated by GRAPH_FIELD_SEP
unique_items = set()
for value in values:
items = str(value).split(GRAPH_FIELD_SEP)
unique_items.update(items)
merged_data[key] = GRAPH_FIELD_SEP.join(unique_items)
elif strategy == "max":
# For numeric fields like weight
try:
merged_data[key] = max(float(v) for v in values)
except (ValueError, TypeError):
merged_data[key] = values[0]
else:
# Default strategy
merged_data[key] = values[0]
return merged_data
async def get_entity_info(
chunk_entity_relation_graph,
entities_vdb,
entity_name: str,
include_vector_data: bool = False,
) -> dict[str, str | None | dict[str, str]]:
"""Get detailed information of an entity"""
# Get information from the graph
node_data = await chunk_entity_relation_graph.get_node(entity_name)
source_id = node_data.get("source_id") if node_data else None
result: dict[str, str | None | dict[str, str]] = {
"entity_name": entity_name,
"source_id": source_id,
"graph_data": node_data,
}
# Optional: Get vector database information
if include_vector_data:
entity_id = compute_mdhash_id(entity_name, prefix="ent-")
vector_data = await entities_vdb.get_by_id(entity_id)
result["vector_data"] = vector_data
return result
async def get_relation_info(
chunk_entity_relation_graph,
relationships_vdb,
src_entity: str,
tgt_entity: str,
include_vector_data: bool = False,
) -> dict[str, str | None | dict[str, str]]:
"""
Get detailed information of a relationship between two entities.
Relationship is unidirectional, swap src_entity and tgt_entity does not change the relationship.
Args:
src_entity: Source entity name
tgt_entity: Target entity name
include_vector_data: Whether to include vector database information
Returns:
Dictionary containing relationship information
"""
# Get information from the graph
edge_data = await chunk_entity_relation_graph.get_edge(src_entity, tgt_entity)
source_id = edge_data.get("source_id") if edge_data else None
result: dict[str, str | None | dict[str, str]] = {
"src_entity": src_entity,
"tgt_entity": tgt_entity,
"source_id": source_id,
"graph_data": edge_data,
}
# Optional: Get vector database information
if include_vector_data:
rel_id = compute_mdhash_id(src_entity + tgt_entity, prefix="rel-")
vector_data = await relationships_vdb.get_by_id(rel_id)
result["vector_data"] = vector_data
return result