Source code for langchain_community.vectorstores.tiledb

"""Wrapper around TileDB vector database."""

from __future__ import annotations

import pickle
import random
import sys
from typing import Any, Dict, Iterable, List, Mapping, Optional, Tuple

import numpy as np
from langchain_core.documents import Document
from langchain_core.embeddings import Embeddings
from langchain_core.utils import guard_import
from langchain_core.vectorstores import VectorStore

from langchain_community.vectorstores.utils import maximal_marginal_relevance

INDEX_METRICS = frozenset(["euclidean"])
DEFAULT_METRIC = "euclidean"
DOCUMENTS_ARRAY_NAME = "documents"
VECTOR_INDEX_NAME = "vectors"
MAX_UINT64 = np.iinfo(np.dtype("uint64")).max
MAX_FLOAT_32 = np.finfo(np.dtype("float32")).max
MAX_FLOAT = sys.float_info.max


[docs]def dependable_tiledb_import() -> Any: """Import tiledb-vector-search if available, otherwise raise error.""" return ( guard_import("tiledb.vector_search"), guard_import("tiledb"), )
[docs]def get_vector_index_uri_from_group(group: Any) -> str: """Get the URI of the vector index.""" return group[VECTOR_INDEX_NAME].uri
[docs]def get_documents_array_uri_from_group(group: Any) -> str: """Get the URI of the documents array from group. Args: group: TileDB group object. Returns: URI of the documents array. """ return group[DOCUMENTS_ARRAY_NAME].uri
[docs]def get_vector_index_uri(uri: str) -> str: """Get the URI of the vector index.""" return f"{uri}/{VECTOR_INDEX_NAME}"
[docs]def get_documents_array_uri(uri: str) -> str: """Get the URI of the documents array.""" return f"{uri}/{DOCUMENTS_ARRAY_NAME}"
[docs]class TileDB(VectorStore): """TileDB vector store. To use, you should have the ``tiledb-vector-search`` python package installed. Example: .. code-block:: python from langchain_community import TileDB embeddings = OpenAIEmbeddings() db = TileDB(embeddings, index_uri, metric) """
[docs] def __init__( self, embedding: Embeddings, index_uri: str, metric: str, *, vector_index_uri: str = "", docs_array_uri: str = "", config: Optional[Mapping[str, Any]] = None, timestamp: Any = None, allow_dangerous_deserialization: bool = False, **kwargs: Any, ): """Initialize with necessary components. Args: allow_dangerous_deserialization: whether to allow deserialization of the data which involves loading data using pickle. data can be modified by malicious actors to deliver a malicious payload that results in execution of arbitrary code on your machine. """ if not allow_dangerous_deserialization: raise ValueError( "TileDB relies on pickle for serialization and deserialization. " "This can be dangerous if the data is intercepted and/or modified " "by malicious actors prior to being de-serialized. " "If you are sure that the data is safe from modification, you can " " set allow_dangerous_deserialization=True to proceed. " "Loading of compromised data using pickle can result in execution of " "arbitrary code on your machine." ) self.embedding = embedding self.embedding_function = embedding.embed_query self.index_uri = index_uri self.metric = metric self.config = config tiledb_vs, tiledb = ( guard_import("tiledb.vector_search"), guard_import("tiledb"), ) with tiledb.scope_ctx(ctx_or_config=config): index_group = tiledb.Group(self.index_uri, "r") self.vector_index_uri = ( vector_index_uri if vector_index_uri != "" else get_vector_index_uri_from_group(index_group) ) self.docs_array_uri = ( docs_array_uri if docs_array_uri != "" else get_documents_array_uri_from_group(index_group) ) index_group.close() group = tiledb.Group(self.vector_index_uri, "r") self.index_type = group.meta.get("index_type") group.close() self.timestamp = timestamp if self.index_type == "FLAT": self.vector_index = tiledb_vs.flat_index.FlatIndex( uri=self.vector_index_uri, config=self.config, timestamp=self.timestamp, **kwargs, ) elif self.index_type == "IVF_FLAT": self.vector_index = tiledb_vs.ivf_flat_index.IVFFlatIndex( uri=self.vector_index_uri, config=self.config, timestamp=self.timestamp, **kwargs, )
@property def embeddings(self) -> Optional[Embeddings]: return self.embedding
[docs] def process_index_results( self, ids: List[int], scores: List[float], *, k: int = 4, filter: Optional[Dict[str, Any]] = None, score_threshold: float = MAX_FLOAT, ) -> List[Tuple[Document, float]]: """Turns TileDB results into a list of documents and scores. Args: ids: List of indices of the documents in the index. scores: List of distances of the documents in the index. k: Number of Documents to return. Defaults to 4. filter (Optional[Dict[str, Any]]): Filter by metadata. Defaults to None. score_threshold: Optional, a floating point value to filter the resulting set of retrieved docs Returns: List of Documents and scores. """ tiledb = guard_import("tiledb") docs = [] docs_array = tiledb.open( self.docs_array_uri, "r", timestamp=self.timestamp, config=self.config ) for idx, score in zip(ids, scores): if idx == 0 and score == 0: continue if idx == MAX_UINT64 and score == MAX_FLOAT_32: continue doc = docs_array[idx] if doc is None or len(doc["text"]) == 0: raise ValueError(f"Could not find document for id {idx}, got {doc}") pickled_metadata = doc.get("metadata") result_doc = Document(page_content=str(doc["text"][0])) if pickled_metadata is not None: metadata = pickle.loads( np.array(pickled_metadata.tolist()).astype(np.uint8).tobytes() ) result_doc.metadata = metadata if filter is not None: filter = { key: [value] if not isinstance(value, list) else value for key, value in filter.items() } if all( result_doc.metadata.get(key) in value for key, value in filter.items() ): docs.append((result_doc, score)) else: docs.append((result_doc, score)) docs_array.close() docs = [(doc, score) for doc, score in docs if score <= score_threshold] return docs[:k]
[docs] def similarity_search_with_score_by_vector( self, embedding: List[float], *, k: int = 4, filter: Optional[Dict[str, Any]] = None, fetch_k: int = 20, **kwargs: Any, ) -> List[Tuple[Document, float]]: """Return docs most similar to query. Args: embedding: Embedding vector to look up documents similar to. k: Number of Documents to return. Defaults to 4. filter (Optional[Dict[str, Any]]): Filter by metadata. Defaults to None. fetch_k: (Optional[int]) Number of Documents to fetch before filtering. Defaults to 20. **kwargs: kwargs to be passed to similarity search. Can include: nprobe: Optional, number of partitions to check if using IVF_FLAT index score_threshold: Optional, a floating point value to filter the resulting set of retrieved docs Returns: List of documents most similar to the query text and distance in float for each. Lower score represents more similarity. """ if "score_threshold" in kwargs: score_threshold = kwargs.pop("score_threshold") else: score_threshold = MAX_FLOAT d, i = self.vector_index.query( np.array([np.array(embedding).astype(np.float32)]).astype(np.float32), k=k if filter is None else fetch_k, **kwargs, ) return self.process_index_results( ids=i[0], scores=d[0], filter=filter, k=k, score_threshold=score_threshold )
[docs] def similarity_search_with_score( self, query: str, *, k: int = 4, filter: Optional[Dict[str, Any]] = None, fetch_k: int = 20, **kwargs: Any, ) -> List[Tuple[Document, float]]: """Return docs most similar to query. Args: query: Text to look up documents similar to. k: Number of Documents to return. Defaults to 4. filter (Optional[Dict[str, str]]): Filter by metadata. Defaults to None. fetch_k: (Optional[int]) Number of Documents to fetch before filtering. Defaults to 20. Returns: List of documents most similar to the query text with Distance as float. Lower score represents more similarity. """ embedding = self.embedding_function(query) docs = self.similarity_search_with_score_by_vector( embedding, k=k, filter=filter, fetch_k=fetch_k, **kwargs, ) return docs
[docs] def similarity_search_by_vector( self, embedding: List[float], k: int = 4, filter: Optional[Dict[str, Any]] = None, fetch_k: int = 20, **kwargs: Any, ) -> List[Document]: """Return docs most similar to embedding vector. Args: embedding: Embedding to look up documents similar to. k: Number of Documents to return. Defaults to 4. filter (Optional[Dict[str, str]]): Filter by metadata. Defaults to None. fetch_k: (Optional[int]) Number of Documents to fetch before filtering. Defaults to 20. Returns: List of Documents most similar to the embedding. """ docs_and_scores = self.similarity_search_with_score_by_vector( embedding, k=k, filter=filter, fetch_k=fetch_k, **kwargs, ) return [doc for doc, _ in docs_and_scores]
[docs] def max_marginal_relevance_search_with_score_by_vector( self, embedding: List[float], *, k: int = 4, fetch_k: int = 20, lambda_mult: float = 0.5, filter: Optional[Dict[str, Any]] = None, **kwargs: Any, ) -> List[Tuple[Document, float]]: """Return docs and their similarity scores selected using the maximal marginal relevance. Maximal marginal relevance optimizes for similarity to query AND diversity among selected documents. Args: embedding: Embedding to look up documents similar to. k: Number of Documents to return. Defaults to 4. fetch_k: Number of Documents to fetch before filtering to pass to MMR algorithm. lambda_mult: Number between 0 and 1 that determines the degree of diversity among the results with 0 corresponding to maximum diversity and 1 to minimum diversity. Defaults to 0.5. Returns: List of Documents and similarity scores selected by maximal marginal relevance and score for each. """ if "score_threshold" in kwargs: score_threshold = kwargs.pop("score_threshold") else: score_threshold = MAX_FLOAT scores, indices = self.vector_index.query( np.array([np.array(embedding).astype(np.float32)]).astype(np.float32), k=fetch_k if filter is None else fetch_k * 2, **kwargs, ) results = self.process_index_results( ids=indices[0], scores=scores[0], filter=filter, k=fetch_k if filter is None else fetch_k * 2, score_threshold=score_threshold, ) embeddings = [ self.embedding.embed_documents([doc.page_content])[0] for doc, _ in results ] mmr_selected = maximal_marginal_relevance( np.array([embedding], dtype=np.float32), embeddings, k=k, lambda_mult=lambda_mult, ) docs_and_scores = [] for i in mmr_selected: docs_and_scores.append(results[i]) return docs_and_scores
[docs] def max_marginal_relevance_search_by_vector( self, embedding: List[float], k: int = 4, fetch_k: int = 20, lambda_mult: float = 0.5, filter: Optional[Dict[str, Any]] = None, **kwargs: Any, ) -> List[Document]: """Return docs selected using the maximal marginal relevance. Maximal marginal relevance optimizes for similarity to query AND diversity among selected documents. Args: embedding: Embedding to look up documents similar to. k: Number of Documents to return. Defaults to 4. fetch_k: Number of Documents to fetch before filtering to pass to MMR algorithm. lambda_mult: Number between 0 and 1 that determines the degree of diversity among the results with 0 corresponding to maximum diversity and 1 to minimum diversity. Defaults to 0.5. Returns: List of Documents selected by maximal marginal relevance. """ docs_and_scores = self.max_marginal_relevance_search_with_score_by_vector( embedding, k=k, fetch_k=fetch_k, lambda_mult=lambda_mult, filter=filter, **kwargs, ) return [doc for doc, _ in docs_and_scores]
[docs] @classmethod def create( cls, index_uri: str, index_type: str, dimensions: int, vector_type: np.dtype, *, metadatas: bool = True, config: Optional[Mapping[str, Any]] = None, ) -> None: tiledb_vs, tiledb = ( guard_import("tiledb.vector_search"), guard_import("tiledb"), ) with tiledb.scope_ctx(ctx_or_config=config): try: tiledb.group_create(index_uri) except tiledb.TileDBError as err: raise err group = tiledb.Group(index_uri, "w") vector_index_uri = get_vector_index_uri(group.uri) docs_uri = get_documents_array_uri(group.uri) if index_type == "FLAT": tiledb_vs.flat_index.create( uri=vector_index_uri, dimensions=dimensions, vector_type=vector_type, config=config, ) elif index_type == "IVF_FLAT": tiledb_vs.ivf_flat_index.create( uri=vector_index_uri, dimensions=dimensions, vector_type=vector_type, config=config, ) group.add(vector_index_uri, name=VECTOR_INDEX_NAME) # Create TileDB array to store Documents # TODO add a Document store API to tiledb-vector-search to allow storing # different types of objects and metadata in a more generic way. dim = tiledb.Dim( name="id", domain=(0, MAX_UINT64 - 1), dtype=np.dtype(np.uint64), ) dom = tiledb.Domain(dim) text_attr = tiledb.Attr(name="text", dtype=np.dtype("U1"), var=True) attrs = [text_attr] if metadatas: metadata_attr = tiledb.Attr(name="metadata", dtype=np.uint8, var=True) attrs.append(metadata_attr) schema = tiledb.ArraySchema( domain=dom, sparse=True, allows_duplicates=False, attrs=attrs, ) tiledb.Array.create(docs_uri, schema) group.add(docs_uri, name=DOCUMENTS_ARRAY_NAME) group.close()
@classmethod def __from( cls, texts: List[str], embeddings: List[List[float]], embedding: Embeddings, index_uri: str, *, metadatas: Optional[List[dict]] = None, ids: Optional[List[str]] = None, metric: str = DEFAULT_METRIC, index_type: str = "FLAT", config: Optional[Mapping[str, Any]] = None, index_timestamp: int = 0, **kwargs: Any, ) -> TileDB: if metric not in INDEX_METRICS: raise ValueError( ( f"Unsupported distance metric: {metric}. " f"Expected one of {list(INDEX_METRICS)}" ) ) tiledb_vs, tiledb = ( guard_import("tiledb.vector_search"), guard_import("tiledb"), ) input_vectors = np.array(embeddings).astype(np.float32) cls.create( index_uri=index_uri, index_type=index_type, dimensions=input_vectors.shape[1], vector_type=input_vectors.dtype, metadatas=metadatas is not None, config=config, ) with tiledb.scope_ctx(ctx_or_config=config): if not embeddings: raise ValueError("embeddings must be provided to build a TileDB index") vector_index_uri = get_vector_index_uri(index_uri) docs_uri = get_documents_array_uri(index_uri) if ids is None: ids = [str(random.randint(0, MAX_UINT64 - 1)) for _ in texts] external_ids = np.array(ids).astype(np.uint64) tiledb_vs.ingestion.ingest( index_type=index_type, index_uri=vector_index_uri, input_vectors=input_vectors, external_ids=external_ids, index_timestamp=index_timestamp if index_timestamp != 0 else None, config=config, **kwargs, ) with tiledb.open(docs_uri, "w") as A: if external_ids is None: external_ids = np.zeros(len(texts), dtype=np.uint64) for i in range(len(texts)): external_ids[i] = i data = {} data["text"] = np.array(texts) if metadatas is not None: metadata_attr = np.empty([len(metadatas)], dtype=object) i = 0 for metadata in metadatas: metadata_attr[i] = np.frombuffer( pickle.dumps(metadata), dtype=np.uint8 ) i += 1 data["metadata"] = metadata_attr A[external_ids] = data return cls( embedding=embedding, index_uri=index_uri, metric=metric, config=config, **kwargs, )
[docs] def delete( self, ids: Optional[List[str]] = None, timestamp: int = 0, **kwargs: Any ) -> Optional[bool]: """Delete by vector ID or other criteria. Args: ids: List of ids to delete. timestamp: Optional timestamp to delete with. **kwargs: Other keyword arguments that subclasses might use. Returns: Optional[bool]: True if deletion is successful, False otherwise, None if not implemented. """ external_ids = np.array(ids).astype(np.uint64) self.vector_index.delete_batch( external_ids=external_ids, timestamp=timestamp if timestamp != 0 else None ) return True
[docs] def add_texts( self, texts: Iterable[str], metadatas: Optional[List[dict]] = None, ids: Optional[List[str]] = None, timestamp: int = 0, **kwargs: Any, ) -> List[str]: """Run more texts through the embeddings and add to the vectorstore. Args: texts: Iterable of strings to add to the vectorstore. metadatas: Optional list of metadatas associated with the texts. ids: Optional ids of each text object. timestamp: Optional timestamp to write new texts with. kwargs: vectorstore specific parameters Returns: List of ids from adding the texts into the vectorstore. """ tiledb = guard_import("tiledb") embeddings = self.embedding.embed_documents(list(texts)) if ids is None: ids = [str(random.randint(0, MAX_UINT64 - 1)) for _ in texts] external_ids = np.array(ids).astype(np.uint64) vectors = np.empty((len(embeddings)), dtype="O") for i in range(len(embeddings)): vectors[i] = np.array(embeddings[i], dtype=np.float32) self.vector_index.update_batch( vectors=vectors, external_ids=external_ids, timestamp=timestamp if timestamp != 0 else None, ) docs = {} docs["text"] = np.array(texts) if metadatas is not None: metadata_attr = np.empty([len(metadatas)], dtype=object) i = 0 for metadata in metadatas: metadata_attr[i] = np.frombuffer(pickle.dumps(metadata), dtype=np.uint8) i += 1 docs["metadata"] = metadata_attr docs_array = tiledb.open( self.docs_array_uri, "w", timestamp=timestamp if timestamp != 0 else None, config=self.config, ) docs_array[external_ids] = docs docs_array.close() return ids
[docs] @classmethod def from_texts( cls, texts: List[str], embedding: Embeddings, metadatas: Optional[List[dict]] = None, ids: Optional[List[str]] = None, metric: str = DEFAULT_METRIC, index_uri: str = "/tmp/tiledb_array", index_type: str = "FLAT", config: Optional[Mapping[str, Any]] = None, index_timestamp: int = 0, **kwargs: Any, ) -> TileDB: """Construct a TileDB index from raw documents. Args: texts: List of documents to index. embedding: Embedding function to use. metadatas: List of metadata dictionaries to associate with documents. ids: Optional ids of each text object. metric: Metric to use for indexing. Defaults to "euclidean". index_uri: The URI to write the TileDB arrays index_type: Optional, Vector index type ("FLAT", IVF_FLAT") config: Optional, TileDB config index_timestamp: Optional, timestamp to write new texts with. Example: .. code-block:: python from langchain_community import TileDB from langchain_community.embeddings import OpenAIEmbeddings embeddings = OpenAIEmbeddings() index = TileDB.from_texts(texts, embeddings) """ embeddings = [] embeddings = embedding.embed_documents(texts) return cls.__from( texts=texts, embeddings=embeddings, embedding=embedding, metadatas=metadatas, ids=ids, metric=metric, index_uri=index_uri, index_type=index_type, config=config, index_timestamp=index_timestamp, **kwargs, )
[docs] @classmethod def from_embeddings( cls, text_embeddings: List[Tuple[str, List[float]]], embedding: Embeddings, index_uri: str, *, metadatas: Optional[List[dict]] = None, ids: Optional[List[str]] = None, metric: str = DEFAULT_METRIC, index_type: str = "FLAT", config: Optional[Mapping[str, Any]] = None, index_timestamp: int = 0, **kwargs: Any, ) -> TileDB: """Construct TileDB index from embeddings. Args: text_embeddings: List of tuples of (text, embedding) embedding: Embedding function to use. index_uri: The URI to write the TileDB arrays metadatas: List of metadata dictionaries to associate with documents. metric: Optional, Metric to use for indexing. Defaults to "euclidean". index_type: Optional, Vector index type ("FLAT", IVF_FLAT") config: Optional, TileDB config index_timestamp: Optional, timestamp to write new texts with. Example: .. code-block:: python from langchain_community import TileDB from langchain_community.embeddings import OpenAIEmbeddings embeddings = OpenAIEmbeddings() text_embeddings = embeddings.embed_documents(texts) text_embedding_pairs = list(zip(texts, text_embeddings)) db = TileDB.from_embeddings(text_embedding_pairs, embeddings) """ texts = [t[0] for t in text_embeddings] embeddings = [t[1] for t in text_embeddings] return cls.__from( texts=texts, embeddings=embeddings, embedding=embedding, metadatas=metadatas, ids=ids, metric=metric, index_uri=index_uri, index_type=index_type, config=config, index_timestamp=index_timestamp, **kwargs, )
[docs] @classmethod def load( cls, index_uri: str, embedding: Embeddings, *, metric: str = DEFAULT_METRIC, config: Optional[Mapping[str, Any]] = None, timestamp: Any = None, **kwargs: Any, ) -> TileDB: """Load a TileDB index from a URI. Args: index_uri: The URI of the TileDB vector index. embedding: Embeddings to use when generating queries. metric: Optional, Metric to use for indexing. Defaults to "euclidean". config: Optional, TileDB config timestamp: Optional, timestamp to use for opening the arrays. """ return cls( embedding=embedding, index_uri=index_uri, metric=metric, config=config, timestamp=timestamp, **kwargs, )
[docs] def consolidate_updates(self, **kwargs: Any) -> None: self.vector_index = self.vector_index.consolidate_updates(**kwargs)