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import os | |
import shutil | |
from overrides import override | |
import pickle | |
from typing import Dict, List, Optional, Sequence, Set, cast | |
from chromadb.config import System | |
from chromadb.segment.impl.vector.batch import Batch | |
from chromadb.segment.impl.vector.hnsw_params import PersistentHnswParams | |
from chromadb.segment.impl.vector.local_hnsw import ( | |
DEFAULT_CAPACITY, | |
LocalHnswSegment, | |
) | |
from chromadb.segment.impl.vector.brute_force_index import BruteForceIndex | |
from chromadb.telemetry.opentelemetry import ( | |
OpenTelemetryClient, | |
OpenTelemetryGranularity, | |
trace_method, | |
) | |
from chromadb.types import ( | |
EmbeddingRecord, | |
Metadata, | |
Operation, | |
Segment, | |
SeqId, | |
Vector, | |
VectorEmbeddingRecord, | |
VectorQuery, | |
VectorQueryResult, | |
) | |
import hnswlib | |
import logging | |
from chromadb.utils.read_write_lock import ReadRWLock, WriteRWLock | |
logger = logging.getLogger(__name__) | |
class PersistentData: | |
"""Stores the data and metadata needed for a PersistentLocalHnswSegment""" | |
dimensionality: Optional[int] | |
total_elements_added: int | |
max_seq_id: SeqId | |
id_to_label: Dict[str, int] | |
label_to_id: Dict[int, str] | |
id_to_seq_id: Dict[str, SeqId] | |
def __init__( | |
self, | |
dimensionality: Optional[int], | |
total_elements_added: int, | |
max_seq_id: int, | |
id_to_label: Dict[str, int], | |
label_to_id: Dict[int, str], | |
id_to_seq_id: Dict[str, SeqId], | |
): | |
self.dimensionality = dimensionality | |
self.total_elements_added = total_elements_added | |
self.max_seq_id = max_seq_id | |
self.id_to_label = id_to_label | |
self.label_to_id = label_to_id | |
self.id_to_seq_id = id_to_seq_id | |
def load_from_file(filename: str) -> "PersistentData": | |
"""Load persistent data from a file""" | |
with open(filename, "rb") as f: | |
ret = cast(PersistentData, pickle.load(f)) | |
return ret | |
class PersistentLocalHnswSegment(LocalHnswSegment): | |
METADATA_FILE: str = "index_metadata.pickle" | |
# How many records to add to index at once, we do this because crossing the python/c++ boundary is expensive (for add()) | |
# When records are not added to the c++ index, they are buffered in memory and served | |
# via brute force search. | |
_batch_size: int | |
_brute_force_index: Optional[BruteForceIndex] | |
_index_initialized: bool = False | |
_curr_batch: Batch | |
# How many records to add to index before syncing to disk | |
_sync_threshold: int | |
_persist_data: PersistentData | |
_persist_directory: str | |
_allow_reset: bool | |
_opentelemtry_client: OpenTelemetryClient | |
def __init__(self, system: System, segment: Segment): | |
super().__init__(system, segment) | |
self._opentelemtry_client = system.require(OpenTelemetryClient) | |
self._params = PersistentHnswParams(segment["metadata"] or {}) | |
self._batch_size = self._params.batch_size | |
self._sync_threshold = self._params.sync_threshold | |
self._allow_reset = system.settings.allow_reset | |
self._persist_directory = system.settings.require("persist_directory") | |
self._curr_batch = Batch() | |
self._brute_force_index = None | |
if not os.path.exists(self._get_storage_folder()): | |
os.makedirs(self._get_storage_folder(), exist_ok=True) | |
# Load persist data if it exists already, otherwise create it | |
if self._index_exists(): | |
self._persist_data = PersistentData.load_from_file( | |
self._get_metadata_file() | |
) | |
self._dimensionality = self._persist_data.dimensionality | |
self._total_elements_added = self._persist_data.total_elements_added | |
self._max_seq_id = self._persist_data.max_seq_id | |
self._id_to_label = self._persist_data.id_to_label | |
self._label_to_id = self._persist_data.label_to_id | |
self._id_to_seq_id = self._persist_data.id_to_seq_id | |
# If the index was written to, we need to re-initialize it | |
if len(self._id_to_label) > 0: | |
self._dimensionality = cast(int, self._dimensionality) | |
self._init_index(self._dimensionality) | |
else: | |
self._persist_data = PersistentData( | |
self._dimensionality, | |
self._total_elements_added, | |
self._max_seq_id, | |
self._id_to_label, | |
self._label_to_id, | |
self._id_to_seq_id, | |
) | |
def propagate_collection_metadata(metadata: Metadata) -> Optional[Metadata]: | |
# Extract relevant metadata | |
segment_metadata = PersistentHnswParams.extract(metadata) | |
return segment_metadata | |
def _index_exists(self) -> bool: | |
"""Check if the index exists via the metadata file""" | |
return os.path.exists(self._get_metadata_file()) | |
def _get_metadata_file(self) -> str: | |
"""Get the metadata file path""" | |
return os.path.join(self._get_storage_folder(), self.METADATA_FILE) | |
def _get_storage_folder(self) -> str: | |
"""Get the storage folder path""" | |
folder = os.path.join(self._persist_directory, str(self._id)) | |
return folder | |
def _init_index(self, dimensionality: int) -> None: | |
index = hnswlib.Index(space=self._params.space, dim=dimensionality) | |
self._brute_force_index = BruteForceIndex( | |
size=self._batch_size, | |
dimensionality=dimensionality, | |
space=self._params.space, | |
) | |
# Check if index exists and load it if it does | |
if self._index_exists(): | |
index.load_index( | |
self._get_storage_folder(), | |
is_persistent_index=True, | |
max_elements=int( | |
max(self.count() * self._params.resize_factor, DEFAULT_CAPACITY) | |
), | |
) | |
else: | |
index.init_index( | |
max_elements=DEFAULT_CAPACITY, | |
ef_construction=self._params.construction_ef, | |
M=self._params.M, | |
is_persistent_index=True, | |
persistence_location=self._get_storage_folder(), | |
) | |
index.set_ef(self._params.search_ef) | |
index.set_num_threads(self._params.num_threads) | |
self._index = index | |
self._dimensionality = dimensionality | |
self._index_initialized = True | |
def _persist(self) -> None: | |
"""Persist the index and data to disk""" | |
index = cast(hnswlib.Index, self._index) | |
# Persist the index | |
index.persist_dirty() | |
# Persist the metadata | |
self._persist_data.dimensionality = self._dimensionality | |
self._persist_data.total_elements_added = self._total_elements_added | |
self._persist_data.max_seq_id = self._max_seq_id | |
# TODO: This should really be stored in sqlite, the index itself, or a better | |
# storage format | |
self._persist_data.id_to_label = self._id_to_label | |
self._persist_data.label_to_id = self._label_to_id | |
self._persist_data.id_to_seq_id = self._id_to_seq_id | |
with open(self._get_metadata_file(), "wb") as metadata_file: | |
pickle.dump(self._persist_data, metadata_file, pickle.HIGHEST_PROTOCOL) | |
def _apply_batch(self, batch: Batch) -> None: | |
super()._apply_batch(batch) | |
if ( | |
self._total_elements_added - self._persist_data.total_elements_added | |
>= self._sync_threshold | |
): | |
self._persist() | |
def _write_records(self, records: Sequence[EmbeddingRecord]) -> None: | |
"""Add a batch of embeddings to the index""" | |
if not self._running: | |
raise RuntimeError("Cannot add embeddings to stopped component") | |
with WriteRWLock(self._lock): | |
for record in records: | |
if record["embedding"] is not None: | |
self._ensure_index(len(records), len(record["embedding"])) | |
if not self._index_initialized: | |
# If the index is not initialized here, it means that we have | |
# not yet added any records to the index. So we can just | |
# ignore the record since it was a delete. | |
continue | |
self._brute_force_index = cast(BruteForceIndex, self._brute_force_index) | |
self._max_seq_id = max(self._max_seq_id, record["seq_id"]) | |
id = record["id"] | |
op = record["operation"] | |
exists_in_index = self._id_to_label.get( | |
id, None | |
) is not None or self._brute_force_index.has_id(id) | |
exists_in_bf_index = self._brute_force_index.has_id(id) | |
if op == Operation.DELETE: | |
if exists_in_index: | |
self._curr_batch.apply(record) | |
if exists_in_bf_index: | |
self._brute_force_index.delete([record]) | |
else: | |
logger.warning(f"Delete of nonexisting embedding ID: {id}") | |
elif op == Operation.UPDATE: | |
if record["embedding"] is not None: | |
if exists_in_index: | |
self._curr_batch.apply(record) | |
self._brute_force_index.upsert([record]) | |
else: | |
logger.warning( | |
f"Update of nonexisting embedding ID: {record['id']}" | |
) | |
elif op == Operation.ADD: | |
if record["embedding"] is not None: | |
if not exists_in_index: | |
self._curr_batch.apply(record, not exists_in_index) | |
self._brute_force_index.upsert([record]) | |
else: | |
logger.warning(f"Add of existing embedding ID: {id}") | |
elif op == Operation.UPSERT: | |
if record["embedding"] is not None: | |
self._curr_batch.apply(record, exists_in_index) | |
self._brute_force_index.upsert([record]) | |
if len(self._curr_batch) >= self._batch_size: | |
self._apply_batch(self._curr_batch) | |
self._curr_batch = Batch() | |
self._brute_force_index.clear() | |
def count(self) -> int: | |
return ( | |
len(self._id_to_label) | |
+ self._curr_batch.add_count | |
- self._curr_batch.delete_count | |
) | |
def get_vectors( | |
self, ids: Optional[Sequence[str]] = None | |
) -> Sequence[VectorEmbeddingRecord]: | |
"""Get the embeddings from the HNSW index and layered brute force | |
batch index.""" | |
ids_hnsw: Set[str] = set() | |
ids_bf: Set[str] = set() | |
if self._index is not None: | |
ids_hnsw = set(self._id_to_label.keys()) | |
if self._brute_force_index is not None: | |
ids_bf = set(self._curr_batch.get_written_ids()) | |
target_ids = ids or list(ids_hnsw.union(ids_bf)) | |
self._brute_force_index = cast(BruteForceIndex, self._brute_force_index) | |
hnsw_labels = [] | |
results: List[Optional[VectorEmbeddingRecord]] = [] | |
id_to_index: Dict[str, int] = {} | |
for i, id in enumerate(target_ids): | |
if id in ids_bf: | |
results.append(self._brute_force_index.get_vectors([id])[0]) | |
elif id in ids_hnsw and id not in self._curr_batch._deleted_ids: | |
hnsw_labels.append(self._id_to_label[id]) | |
# Placeholder for hnsw results to be filled in down below so we | |
# can batch the hnsw get() call | |
results.append(None) | |
id_to_index[id] = i | |
if len(hnsw_labels) > 0 and self._index is not None: | |
vectors = cast(Sequence[Vector], self._index.get_items(hnsw_labels)) | |
for label, vector in zip(hnsw_labels, vectors): | |
id = self._label_to_id[label] | |
seq_id = self._id_to_seq_id[id] | |
results[id_to_index[id]] = VectorEmbeddingRecord( | |
id=id, seq_id=seq_id, embedding=vector | |
) | |
return results # type: ignore ## Python can't cast List with Optional to List with VectorEmbeddingRecord | |
def query_vectors( | |
self, query: VectorQuery | |
) -> Sequence[Sequence[VectorQueryResult]]: | |
if self._index is None and self._brute_force_index is None: | |
return [[] for _ in range(len(query["vectors"]))] | |
k = query["k"] | |
if k > self.count(): | |
logger.warning( | |
f"Number of requested results {k} is greater than number of elements in index {self.count()}, updating n_results = {self.count()}" | |
) | |
k = self.count() | |
# Overquery by updated and deleted elements layered on the index because they may | |
# hide the real nearest neighbors in the hnsw index | |
hnsw_k = k + self._curr_batch.update_count + self._curr_batch.delete_count | |
if hnsw_k > len(self._id_to_label): | |
hnsw_k = len(self._id_to_label) | |
hnsw_query = VectorQuery( | |
vectors=query["vectors"], | |
k=hnsw_k, | |
allowed_ids=query["allowed_ids"], | |
include_embeddings=query["include_embeddings"], | |
options=query["options"], | |
) | |
# For each query vector, we want to take the top k results from the | |
# combined results of the brute force and hnsw index | |
results: List[List[VectorQueryResult]] = [] | |
self._brute_force_index = cast(BruteForceIndex, self._brute_force_index) | |
with ReadRWLock(self._lock): | |
bf_results = self._brute_force_index.query(query) | |
hnsw_results = super().query_vectors(hnsw_query) | |
for i in range(len(query["vectors"])): | |
# Merge results into a single list of size k | |
bf_pointer: int = 0 | |
hnsw_pointer: int = 0 | |
curr_bf_result: Sequence[VectorQueryResult] = bf_results[i] | |
curr_hnsw_result: Sequence[VectorQueryResult] = hnsw_results[i] | |
curr_results: List[VectorQueryResult] = [] | |
# In the case where filters cause the number of results to be less than k, | |
# we set k to be the number of results | |
total_results = len(curr_bf_result) + len(curr_hnsw_result) | |
if total_results == 0: | |
results.append([]) | |
else: | |
while len(curr_results) < min(k, total_results): | |
if bf_pointer < len(curr_bf_result) and hnsw_pointer < len( | |
curr_hnsw_result | |
): | |
bf_dist = curr_bf_result[bf_pointer]["distance"] | |
hnsw_dist = curr_hnsw_result[hnsw_pointer]["distance"] | |
if bf_dist <= hnsw_dist: | |
curr_results.append(curr_bf_result[bf_pointer]) | |
bf_pointer += 1 | |
else: | |
id = curr_hnsw_result[hnsw_pointer]["id"] | |
# Only add the hnsw result if it is not in the brute force index | |
# as updated or deleted | |
if not self._brute_force_index.has_id( | |
id | |
) and not self._curr_batch.is_deleted(id): | |
curr_results.append(curr_hnsw_result[hnsw_pointer]) | |
hnsw_pointer += 1 | |
else: | |
break | |
remaining = min(k, total_results) - len(curr_results) | |
if remaining > 0 and hnsw_pointer < len(curr_hnsw_result): | |
for i in range( | |
hnsw_pointer, | |
min(len(curr_hnsw_result), hnsw_pointer + remaining + 1), | |
): | |
id = curr_hnsw_result[i]["id"] | |
if not self._brute_force_index.has_id( | |
id | |
) and not self._curr_batch.is_deleted(id): | |
curr_results.append(curr_hnsw_result[i]) | |
elif remaining > 0 and bf_pointer < len(curr_bf_result): | |
curr_results.extend( | |
curr_bf_result[bf_pointer : bf_pointer + remaining] | |
) | |
results.append(curr_results) | |
return results | |
def reset_state(self) -> None: | |
if self._allow_reset: | |
data_path = self._get_storage_folder() | |
if os.path.exists(data_path): | |
self.close_persistent_index() | |
shutil.rmtree(data_path, ignore_errors=True) | |
def delete(self) -> None: | |
data_path = self._get_storage_folder() | |
if os.path.exists(data_path): | |
self.close_persistent_index() | |
shutil.rmtree(data_path, ignore_errors=False) | |
def get_file_handle_count() -> int: | |
"""Return how many file handles are used by the index""" | |
hnswlib_count = hnswlib.Index.file_handle_count | |
hnswlib_count = cast(int, hnswlib_count) | |
# One extra for the metadata file | |
return hnswlib_count + 1 # type: ignore | |
def open_persistent_index(self) -> None: | |
"""Open the persistent index""" | |
if self._index is not None: | |
self._index.open_file_handles() | |
def close_persistent_index(self) -> None: | |
"""Close the persistent index""" | |
if self._index is not None: | |
self._index.close_file_handles() | |