wehub-resource-sync
345 lines
13 KiB
Python
345 lines
13 KiB
Python
import asyncio
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import os
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from dataclasses import dataclass
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from typing import Any, final
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import numpy as np
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from lightrag.base import BaseVectorStorage
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from lightrag.constants import DEFAULT_QUERY_PRIORITY
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from lightrag.utils import logger
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import pipmaster as pm
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if not pm.is_installed("chromadb"):
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pm.install("chromadb")
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from chromadb import HttpClient, PersistentClient # type: ignore
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from chromadb.config import Settings # type: ignore
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@final
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@dataclass
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class ChromaVectorDBStorage(BaseVectorStorage):
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"""ChromaDB vector storage implementation."""
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def __post_init__(self):
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self._validate_embedding_func()
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try:
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config = self.global_config.get("vector_db_storage_cls_kwargs", {})
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cosine_threshold = config.get("cosine_better_than_threshold")
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if cosine_threshold is None:
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raise ValueError(
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"cosine_better_than_threshold must be specified in vector_db_storage_cls_kwargs"
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)
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self.cosine_better_than_threshold = cosine_threshold
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user_collection_settings = config.get("collection_settings", {})
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# Default HNSW index settings for ChromaDB
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default_collection_settings = {
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# Distance metric used for similarity search (cosine similarity)
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"hnsw:space": "cosine",
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# Number of nearest neighbors to explore during index construction
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# Higher values = better recall but slower indexing
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"hnsw:construction_ef": 128,
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# Number of nearest neighbors to explore during search
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# Higher values = better recall but slower search
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"hnsw:search_ef": 128,
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# Number of connections per node in the HNSW graph
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# Higher values = better recall but more memory usage
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"hnsw:M": 16,
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# Number of vectors to process in one batch during indexing
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"hnsw:batch_size": 100,
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# Number of updates before forcing index synchronization
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# Lower values = more frequent syncs but slower indexing
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"hnsw:sync_threshold": 1000,
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}
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collection_settings = {
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**default_collection_settings,
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**user_collection_settings,
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}
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local_path = config.get("local_path", None)
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if local_path:
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self._client = PersistentClient(
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path=local_path,
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settings=Settings(
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allow_reset=True,
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anonymized_telemetry=False,
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),
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)
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else:
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auth_provider = config.get(
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"auth_provider", "chromadb.auth.token_authn.TokenAuthClientProvider"
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)
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auth_credentials = config.get("auth_token", "secret-token")
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headers = {}
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if "token_authn" in auth_provider:
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headers = {
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config.get(
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"auth_header_name", "X-Chroma-Token"
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): auth_credentials
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}
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elif "basic_authn" in auth_provider:
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auth_credentials = config.get("auth_credentials", "admin:admin")
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self._client = HttpClient(
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host=config.get("host", "localhost"),
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port=config.get("port", 8000),
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headers=headers,
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settings=Settings(
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chroma_api_impl="rest",
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chroma_client_auth_provider=auth_provider,
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chroma_client_auth_credentials=auth_credentials,
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allow_reset=True,
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anonymized_telemetry=False,
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),
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)
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self._collection = self._client.get_or_create_collection(
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name=self.namespace,
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metadata={
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**collection_settings,
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"dimension": self.embedding_func.embedding_dim,
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},
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)
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# Use batch size from collection settings if specified
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self._max_batch_size = self.global_config.get(
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"embedding_batch_num", collection_settings.get("hnsw:batch_size", 32)
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)
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except Exception as e:
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logger.error(f"ChromaDB initialization failed: {str(e)}")
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raise
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async def upsert(self, data: dict[str, dict[str, Any]]) -> None:
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logger.debug(f"Inserting {len(data)} to {self.namespace}")
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if not data:
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return
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try:
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import time
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current_time = int(time.time())
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ids = list(data.keys())
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documents = [v["content"] for v in data.values()]
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metadatas = [
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{
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**{k: v for k, v in item.items() if k in self.meta_fields},
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"created_at": current_time,
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}
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or {"_default": "true", "created_at": current_time}
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for item in data.values()
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]
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# Process in batches
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batches = [
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documents[i : i + self._max_batch_size]
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for i in range(0, len(documents), self._max_batch_size)
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]
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embedding_tasks = [self.embedding_func(batch) for batch in batches]
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embeddings_list = []
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# Pre-allocate embeddings_list with known size
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embeddings_list = [None] * len(embedding_tasks)
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# Use asyncio.gather instead of as_completed if order doesn't matter
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embeddings_results = await asyncio.gather(*embedding_tasks)
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embeddings_list = list(embeddings_results)
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embeddings = np.concatenate(embeddings_list)
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# Upsert in batches
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for i in range(0, len(ids), self._max_batch_size):
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batch_slice = slice(i, i + self._max_batch_size)
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self._collection.upsert(
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ids=ids[batch_slice],
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embeddings=embeddings[batch_slice].tolist(),
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documents=documents[batch_slice],
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metadatas=metadatas[batch_slice],
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)
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return ids
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except Exception as e:
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logger.error(f"Error during ChromaDB upsert: {str(e)}")
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raise
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async def query(self, query: str, top_k: int) -> list[dict[str, Any]]:
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try:
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embedding = await self.embedding_func(
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[query], _priority=DEFAULT_QUERY_PRIORITY
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) # higher priority for query
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results = self._collection.query(
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query_embeddings=embedding.tolist()
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if not isinstance(embedding, list)
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else embedding,
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n_results=top_k * 2, # Request more results to allow for filtering
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include=["metadatas", "distances", "documents"],
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)
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# Filter results by cosine similarity threshold and take top k
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# We request 2x results initially to have enough after filtering
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# ChromaDB returns cosine similarity (1 = identical, 0 = orthogonal)
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# We convert to distance (0 = identical, 1 = orthogonal) via (1 - similarity)
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# Only keep results with distance below threshold, then take top k
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return [
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{
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"id": results["ids"][0][i],
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"distance": 1 - results["distances"][0][i],
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"content": results["documents"][0][i],
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"created_at": results["metadatas"][0][i].get("created_at"),
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**results["metadatas"][0][i],
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}
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for i in range(len(results["ids"][0]))
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if (1 - results["distances"][0][i]) >= self.cosine_better_than_threshold
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][:top_k]
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except Exception as e:
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logger.error(f"Error during ChromaDB query: {str(e)}")
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raise
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async def index_done_callback(self) -> None:
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# ChromaDB handles persistence automatically
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pass
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async def delete_entity(self, entity_name: str) -> None:
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"""Delete an entity by its ID.
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Args:
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entity_name: The ID of the entity to delete
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"""
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try:
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logger.info(f"Deleting entity with ID {entity_name} from {self.namespace}")
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self._collection.delete(ids=[entity_name])
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except Exception as e:
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logger.error(f"Error during entity deletion: {str(e)}")
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raise
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async def delete_entity_relation(self, entity_name: str) -> None:
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"""Delete an entity and its relations by ID.
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In vector DB context, this is equivalent to delete_entity.
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Args:
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entity_name: The ID of the entity to delete
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"""
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await self.delete_entity(entity_name)
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async def delete(self, ids: list[str]) -> None:
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"""Delete vectors with specified IDs
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Args:
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ids: List of vector IDs to be deleted
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"""
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try:
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self._collection.delete(ids=ids)
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logger.debug(
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f"Successfully deleted {len(ids)} vectors from {self.namespace}"
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)
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except Exception as e:
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logger.error(f"Error while deleting vectors from {self.namespace}: {e}")
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raise
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except Exception as e:
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logger.error(f"Error during prefix search in ChromaDB: {str(e)}")
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raise
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async def get_by_id(self, id: str) -> dict[str, Any] | None:
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"""Get vector data by its ID
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Args:
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id: The unique identifier of the vector
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Returns:
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The vector data if found, or None if not found
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"""
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try:
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# Query the collection for a single vector by ID
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result = self._collection.get(
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ids=[id], include=["metadatas", "embeddings", "documents"]
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)
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if not result or not result["ids"] or len(result["ids"]) == 0:
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return None
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# Format the result to match the expected structure
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return {
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"id": result["ids"][0],
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"vector": result["embeddings"][0],
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"content": result["documents"][0],
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"created_at": result["metadatas"][0].get("created_at"),
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**result["metadatas"][0],
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}
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except Exception as e:
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logger.error(f"Error retrieving vector data for ID {id}: {e}")
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return None
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async def get_by_ids(self, ids: list[str]) -> list[dict[str, Any]]:
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"""Get multiple vector data by their IDs
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Args:
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ids: List of unique identifiers
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Returns:
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List of vector data objects that were found
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"""
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if not ids:
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return []
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try:
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# Query the collection for multiple vectors by IDs
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result = self._collection.get(
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ids=ids, include=["metadatas", "embeddings", "documents"]
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)
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if not result or not result["ids"] or len(result["ids"]) == 0:
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return []
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# Format the results to match the expected structure and preserve ordering
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formatted_map: dict[str, dict[str, Any]] = {}
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for i, result_id in enumerate(result["ids"]):
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record = {
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"id": result_id,
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"vector": result["embeddings"][i],
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"content": result["documents"][i],
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"created_at": result["metadatas"][i].get("created_at"),
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**result["metadatas"][i],
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}
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formatted_map[str(result_id)] = record
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ordered_results: list[dict[str, Any] | None] = []
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for requested_id in ids:
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ordered_results.append(formatted_map.get(str(requested_id)))
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return ordered_results
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except Exception as e:
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logger.error(f"Error retrieving vector data for IDs {ids}: {e}")
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return []
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async def drop(self) -> dict[str, str]:
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"""Drop all vector data from storage and clean up resources
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This method will delete all documents from the ChromaDB collection.
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Returns:
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dict[str, str]: Operation status and message
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- On success: {"status": "success", "message": "data dropped"}
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- On failure: {"status": "error", "message": "<error details>"}
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"""
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try:
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# Get all IDs in the collection
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result = self._collection.get(include=[])
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if result and result["ids"] and len(result["ids"]) > 0:
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# Delete all documents
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self._collection.delete(ids=result["ids"])
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logger.info(
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f"Process {os.getpid()} drop ChromaDB collection {self.namespace}"
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)
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return {"status": "success", "message": "data dropped"}
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except Exception as e:
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logger.error(f"Error dropping ChromaDB collection {self.namespace}: {e}")
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return {"status": "error", "message": str(e)}
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