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feat: add query_by_embedding_batch (#3546)
* add query_by_embedding_batch * fix mypy * fix pylint * add test * move query_by_embedding_batch to search_engine * fix and add tests * fix pylint * remove Retriever query logs * add test for multimodal batch retrieval * allow for np.ndarray
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tstadel
GitHub
parent
25bf95d47f
commit
c1c1c97bb2
@ -12,7 +12,7 @@ import numpy as np
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from haystack.schema import Document, Label, MultiLabel
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from haystack.nodes.base import BaseComponent
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from haystack.errors import DuplicateDocumentError, DocumentStoreError
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from haystack.errors import DuplicateDocumentError, DocumentStoreError, HaystackError
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from haystack.nodes.preprocessor import PreProcessor
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from haystack.document_stores.utils import eval_data_from_json, eval_data_from_jsonl, squad_json_to_jsonl
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from haystack.utils.labels import aggregate_labels
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@ -359,6 +359,44 @@ class BaseDocumentStore(BaseComponent):
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) -> List[Document]:
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pass
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def query_by_embedding_batch(
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self,
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query_embs: Union[List[np.ndarray], np.ndarray],
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filters: Optional[
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Union[
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Dict[str, Union[Dict, List, str, int, float, bool]],
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List[Dict[str, Union[Dict, List, str, int, float, bool]]],
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]
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] = None,
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top_k: int = 10,
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index: Optional[str] = None,
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return_embedding: Optional[bool] = None,
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headers: Optional[Dict[str, str]] = None,
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scale_score: bool = True,
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) -> List[List[Document]]:
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if isinstance(filters, list):
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if len(filters) != len(query_embs):
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raise HaystackError(
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"Number of filters does not match number of query_embs. Please provide as many filters"
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" as query_embs or a single filter that will be applied to each query_emb."
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)
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else:
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filters = [filters] * len(query_embs) if filters is not None else [{}] * len(query_embs)
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results = []
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for query_emb, filter in zip(query_embs, filters):
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results.append(
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self.query_by_embedding(
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query_emb=query_emb,
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filters=filter,
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top_k=top_k,
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index=index,
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return_embedding=return_embedding,
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headers=headers,
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scale_score=scale_score,
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)
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)
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return results
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@abstractmethod
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def get_label_count(self, index: Optional[str] = None, headers: Optional[Dict[str, str]] = None) -> int:
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pass
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@ -377,29 +377,7 @@ class ElasticsearchDocumentStore(SearchEngineDocumentStore):
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if not self.embedding_field:
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raise RuntimeError("Please specify arg `embedding_field` in ElasticsearchDocumentStore()")
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# +1 in similarity to avoid negative numbers (for cosine sim)
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body = {"size": top_k, "query": self._get_vector_similarity_query(query_emb, top_k)}
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if filters:
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filter_ = {"bool": {"filter": LogicalFilterClause.parse(filters).convert_to_elasticsearch()}}
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if body["query"]["script_score"]["query"] == {"match_all": {}}:
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body["query"]["script_score"]["query"] = filter_
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else:
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body["query"]["script_score"]["query"]["bool"]["filter"]["bool"]["must"].append(filter_)
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excluded_meta_data: Optional[list] = None
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if self.excluded_meta_data:
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excluded_meta_data = deepcopy(self.excluded_meta_data)
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if return_embedding is True and self.embedding_field in excluded_meta_data:
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excluded_meta_data.remove(self.embedding_field)
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elif return_embedding is False and self.embedding_field not in excluded_meta_data:
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excluded_meta_data.append(self.embedding_field)
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elif return_embedding is False:
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excluded_meta_data = [self.embedding_field]
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if excluded_meta_data:
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body["_source"] = {"excludes": excluded_meta_data}
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body = self._construct_dense_query_body(query_emb, filters, top_k, return_embedding)
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logger.debug("Retriever query: %s", body)
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try:
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@ -428,6 +406,37 @@ class ElasticsearchDocumentStore(SearchEngineDocumentStore):
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]
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return documents
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def _construct_dense_query_body(
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self,
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query_emb: np.ndarray,
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filters: Optional[Dict[str, Union[Dict, List, str, int, float, bool]]] = None,
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top_k: int = 10,
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return_embedding: Optional[bool] = None,
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):
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body = {"size": top_k, "query": self._get_vector_similarity_query(query_emb, top_k)}
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if filters:
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filter_ = {"bool": {"filter": LogicalFilterClause.parse(filters).convert_to_elasticsearch()}}
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if body["query"]["script_score"]["query"] == {"match_all": {}}:
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body["query"]["script_score"]["query"] = filter_
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else:
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body["query"]["script_score"]["query"]["bool"]["filter"]["bool"]["must"].append(filter_)
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excluded_meta_data: Optional[list] = None
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if self.excluded_meta_data:
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excluded_meta_data = deepcopy(self.excluded_meta_data)
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if return_embedding is True and self.embedding_field in excluded_meta_data:
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excluded_meta_data.remove(self.embedding_field)
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elif return_embedding is False and self.embedding_field not in excluded_meta_data:
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excluded_meta_data.append(self.embedding_field)
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elif return_embedding is False:
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excluded_meta_data = [self.embedding_field]
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if excluded_meta_data:
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body["_source"] = {"excludes": excluded_meta_data}
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return body
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def _create_document_index(self, index_name: str, headers: Optional[Dict[str, str]] = None):
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"""
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Create a new index for storing documents. In case if an index with the name already exists, it ensures that
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@ -439,7 +439,28 @@ class OpenSearchDocumentStore(SearchEngineDocumentStore):
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if not self.embedding_field:
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raise DocumentStoreError("Please set a valid `embedding_field` for OpenSearchDocumentStore")
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# +1 in similarity to avoid negative numbers (for cosine sim)
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body = self._construct_dense_query_body(
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query_emb=query_emb, filters=filters, top_k=top_k, return_embedding=return_embedding
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)
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logger.debug("Retriever query: %s", body)
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result = self.client.search(index=index, body=body, request_timeout=300, headers=headers)["hits"]["hits"]
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documents = [
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self._convert_es_hit_to_document(
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hit, adapt_score_for_embedding=True, return_embedding=return_embedding, scale_score=scale_score
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)
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for hit in result
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]
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return documents
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def _construct_dense_query_body(
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self,
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query_emb: np.ndarray,
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filters: Optional[Dict[str, Union[Dict, List, str, int, float, bool]]] = None,
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top_k: int = 10,
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return_embedding: Optional[bool] = None,
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):
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body: Dict[str, Any] = {"size": top_k, "query": self._get_vector_similarity_query(query_emb, top_k)}
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if filters:
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filter_ = LogicalFilterClause.parse(filters).convert_to_elasticsearch()
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@ -450,7 +471,6 @@ class OpenSearchDocumentStore(SearchEngineDocumentStore):
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body["query"]["bool"]["filter"] = filter_
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excluded_meta_data: Optional[list] = None
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if self.excluded_meta_data:
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excluded_meta_data = deepcopy(self.excluded_meta_data)
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@ -463,17 +483,7 @@ class OpenSearchDocumentStore(SearchEngineDocumentStore):
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if excluded_meta_data:
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body["_source"] = {"excludes": excluded_meta_data}
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logger.debug("Retriever query: %s", body)
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result = self.client.search(index=index, body=body, request_timeout=300, headers=headers)["hits"]["hits"]
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documents = [
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self._convert_es_hit_to_document(
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hit, adapt_score_for_embedding=True, return_embedding=return_embedding, scale_score=scale_score
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)
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for hit in result
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]
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return documents
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return body
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def _create_document_index(self, index_name: str, headers: Optional[Dict[str, str]] = None):
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"""
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@ -1,3 +1,5 @@
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# pylint: disable=too-many-public-methods
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from typing import List, Optional, Union, Dict, Any, Generator
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from abc import abstractmethod
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import json
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@ -873,7 +875,6 @@ class SearchEngineDocumentStore(KeywordDocumentStore):
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all_terms_must_match=all_terms_must_match,
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)
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logger.debug("Retriever query: %s", body)
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result = self.client.search(index=index, body=body, headers=headers)["hits"]["hits"]
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documents = [
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@ -1012,7 +1013,6 @@ class SearchEngineDocumentStore(KeywordDocumentStore):
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body.append(headers)
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body.append(cur_query_body)
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logger.debug("Retriever query: %s", body)
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responses = self.client.msearch(index=index, body=body)
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all_documents = []
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@ -1142,6 +1142,155 @@ class SearchEngineDocumentStore(KeywordDocumentStore):
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) from e
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return document
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def query_by_embedding_batch(
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self,
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query_embs: Union[List[np.ndarray], np.ndarray],
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filters: Optional[
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Union[
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Dict[str, Union[Dict, List, str, int, float, bool]],
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List[Dict[str, Union[Dict, List, str, int, float, bool]]],
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]
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] = None,
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top_k: int = 10,
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index: Optional[str] = None,
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return_embedding: Optional[bool] = None,
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headers: Optional[Dict[str, str]] = None,
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scale_score: bool = True,
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) -> List[List[Document]]:
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"""
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Find the documents that are most similar to the provided `query_embs` by using a vector similarity metric.
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:param query_embs: Embeddings of the queries (e.g. gathered from DPR).
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Can be a list of one-dimensional numpy arrays or a two-dimensional numpy array.
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:param filters: Optional filters to narrow down the search space to documents whose metadata fulfill certain
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conditions.
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Filters are defined as nested dictionaries. The keys of the dictionaries can be a logical
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operator (`"$and"`, `"$or"`, `"$not"`), a comparison operator (`"$eq"`, `"$in"`, `"$gt"`,
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`"$gte"`, `"$lt"`, `"$lte"`) or a metadata field name.
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Logical operator keys take a dictionary of metadata field names and/or logical operators as
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value. Metadata field names take a dictionary of comparison operators as value. Comparison
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operator keys take a single value or (in case of `"$in"`) a list of values as value.
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If no logical operator is provided, `"$and"` is used as default operation. If no comparison
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operator is provided, `"$eq"` (or `"$in"` if the comparison value is a list) is used as default
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operation.
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__Example__:
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```python
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filters = {
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"$and": {
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"type": {"$eq": "article"},
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"date": {"$gte": "2015-01-01", "$lt": "2021-01-01"},
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"rating": {"$gte": 3},
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"$or": {
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"genre": {"$in": ["economy", "politics"]},
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"publisher": {"$eq": "nytimes"}
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}
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}
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}
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# or simpler using default operators
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filters = {
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"type": "article",
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"date": {"$gte": "2015-01-01", "$lt": "2021-01-01"},
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"rating": {"$gte": 3},
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"$or": {
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"genre": ["economy", "politics"],
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"publisher": "nytimes"
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}
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}
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```
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To use the same logical operator multiple times on the same level, logical operators take
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optionally a list of dictionaries as value.
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__Example__:
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```python
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filters = {
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"$or": [
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{
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"$and": {
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"Type": "News Paper",
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"Date": {
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"$lt": "2019-01-01"
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}
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}
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},
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{
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"$and": {
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"Type": "Blog Post",
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"Date": {
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"$gte": "2019-01-01"
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}
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}
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}
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]
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}
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```
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:param top_k: How many documents to return
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:param index: Index name for storing the docs and metadata
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:param return_embedding: To return document embedding
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:param headers: Custom HTTP headers to pass to elasticsearch client (e.g. {'Authorization': 'Basic YWRtaW46cm9vdA=='})
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Check out https://www.elastic.co/guide/en/elasticsearch/reference/current/http-clients.html for more information.
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:param scale_score: Whether to scale the similarity score to the unit interval (range of [0,1]).
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If true (default) similarity scores (e.g. cosine or dot_product) which naturally have a different value range will be scaled to a range of [0,1], where 1 means extremely relevant.
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Otherwise raw similarity scores (e.g. cosine or dot_product) will be used.
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:return:
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"""
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if index is None:
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index = self.index
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if return_embedding is None:
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return_embedding = self.return_embedding
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if headers is None:
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headers = {}
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if not self.embedding_field:
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raise DocumentStoreError("Please set a valid `embedding_field` for OpenSearchDocumentStore")
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if isinstance(filters, list):
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if len(filters) != len(query_embs):
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raise HaystackError(
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"Number of filters does not match number of query_embs. Please provide as many filters"
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" as query_embs or a single filter that will be applied to each query_emb."
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)
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else:
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filters = [filters] * len(query_embs) if filters is not None else [{}] * len(query_embs)
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body = []
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for query_emb, cur_filters in zip(query_embs, filters):
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cur_query_body = self._construct_dense_query_body(
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query_emb=query_emb, filters=cur_filters, top_k=top_k, return_embedding=return_embedding
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)
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body.append(headers)
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body.append(cur_query_body)
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logger.debug("Retriever query: %s", body)
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responses = self.client.msearch(index=index, body=body)
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all_documents = []
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cur_documents = []
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for response in responses["responses"]:
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cur_result = response["hits"]["hits"]
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cur_documents = [
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self._convert_es_hit_to_document(
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hit, adapt_score_for_embedding=True, return_embedding=self.return_embedding, scale_score=scale_score
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)
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for hit in cur_result
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]
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all_documents.append(cur_documents)
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return all_documents
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@abstractmethod
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def _construct_dense_query_body(
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self,
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query_emb: np.ndarray,
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filters: Optional[Dict[str, Union[Dict, List, str, int, float, bool]]] = None,
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top_k: int = 10,
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return_embedding: Optional[bool] = None,
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):
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pass
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def update_embeddings(
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self,
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retriever: DenseRetriever,
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@ -467,22 +467,12 @@ class DensePassageRetriever(DenseRetriever):
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if scale_score is None:
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scale_score = self.scale_score
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documents = []
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query_embs: List[np.ndarray] = []
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for batch in self._get_batches(queries=queries, batch_size=batch_size):
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query_embs.extend(self.embed_queries(queries=batch))
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for query_emb, cur_filters in tqdm(
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zip(query_embs, filters), total=len(query_embs), disable=not self.progress_bar, desc="Querying"
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):
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cur_docs = document_store.query_by_embedding(
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query_emb=query_emb,
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top_k=top_k,
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filters=cur_filters,
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index=index,
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headers=headers,
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scale_score=scale_score,
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documents = document_store.query_by_embedding_batch(
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query_embs=query_embs, top_k=top_k, filters=filters, index=index, headers=headers, scale_score=scale_score
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)
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documents.append(cur_docs)
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return documents
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@ -1111,22 +1101,12 @@ class TableTextRetriever(DenseRetriever):
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if scale_score is None:
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scale_score = self.scale_score
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documents = []
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query_embs: List[np.ndarray] = []
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for batch in self._get_batches(queries=queries, batch_size=batch_size):
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query_embs.extend(self.embed_queries(queries=batch))
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for query_emb, cur_filters in tqdm(
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zip(query_embs, filters), total=len(query_embs), disable=not self.progress_bar, desc="Querying"
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):
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cur_docs = document_store.query_by_embedding(
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query_emb=query_emb,
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top_k=top_k,
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filters=cur_filters,
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index=index,
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headers=headers,
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scale_score=scale_score,
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documents = document_store.query_by_embedding_batch(
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query_embs=query_embs, top_k=top_k, filters=filters, index=index, headers=headers, scale_score=scale_score
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)
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documents.append(cur_docs)
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return documents
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@ -1823,22 +1803,12 @@ class EmbeddingRetriever(DenseRetriever):
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if scale_score is None:
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scale_score = self.scale_score
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documents = []
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query_embs: List[np.ndarray] = []
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for batch in self._get_batches(queries=queries, batch_size=batch_size):
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query_embs.extend(self.embed_queries(queries=batch))
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for query_emb, cur_filters in tqdm(
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zip(query_embs, filters), total=len(query_embs), disable=not self.progress_bar, desc="Querying"
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):
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cur_docs = document_store.query_by_embedding(
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query_emb=query_emb,
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top_k=top_k,
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filters=cur_filters,
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index=index,
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headers=headers,
|
||||
scale_score=scale_score,
|
||||
documents = document_store.query_by_embedding_batch(
|
||||
query_embs=query_embs, top_k=top_k, filters=filters, index=index, headers=headers, scale_score=scale_score
|
||||
)
|
||||
documents.append(cur_docs)
|
||||
|
||||
return documents
|
||||
|
||||
@ -2301,9 +2271,8 @@ class MultihopEmbeddingRetriever(EmbeddingRetriever):
|
||||
for it in range(self.num_iterations):
|
||||
texts = [self._merge_query_and_context(q, c) for q, c in zip(batch, context_docs)]
|
||||
query_embs = self.embed_queries(texts)
|
||||
for idx, emb in enumerate(query_embs):
|
||||
cur_docs = document_store.query_by_embedding(
|
||||
query_emb=emb,
|
||||
cur_docs_batch = document_store.query_by_embedding_batch(
|
||||
query_embs=query_embs,
|
||||
top_k=top_k,
|
||||
filters=cur_filters,
|
||||
index=index,
|
||||
@ -2312,11 +2281,12 @@ class MultihopEmbeddingRetriever(EmbeddingRetriever):
|
||||
)
|
||||
if it < self.num_iterations - 1:
|
||||
# add doc with highest score to context
|
||||
for idx, cur_docs in enumerate(cur_docs_batch):
|
||||
if len(cur_docs) > 0:
|
||||
context_docs[idx].append(cur_docs[0])
|
||||
else:
|
||||
# documents in the last iteration are final results
|
||||
documents.append(cur_docs)
|
||||
documents.extend(cur_docs_batch)
|
||||
pb.update(len(batch))
|
||||
pb.close()
|
||||
|
||||
|
||||
@ -205,18 +205,15 @@ class MultiModalRetriever(DenseRetriever):
|
||||
query_embeddings = self.query_embedder.embed(documents=query_docs, batch_size=batch_size)
|
||||
|
||||
# Query documents by embedding (the actual retrieval step)
|
||||
documents = []
|
||||
for query_embedding, query_filters in zip(query_embeddings, filters_list):
|
||||
docs = document_store.query_by_embedding(
|
||||
query_emb=query_embedding,
|
||||
documents = document_store.query_by_embedding_batch(
|
||||
query_embs=query_embeddings,
|
||||
top_k=top_k,
|
||||
filters=query_filters,
|
||||
filters=filters_list, # type: ignore
|
||||
index=index,
|
||||
headers=headers,
|
||||
scale_score=scale_score,
|
||||
)
|
||||
|
||||
documents.append(docs)
|
||||
return documents
|
||||
|
||||
def embed_documents(self, docs: List[Document]) -> np.ndarray:
|
||||
|
||||
@ -685,14 +685,12 @@ class MostSimilarDocumentsPipeline(BaseStandardPipeline):
|
||||
:param top_k: How many documents id to return against single document
|
||||
:param index: Optionally specify the name of index to query the document from. If None, the DocumentStore's default index (self.index) will be used.
|
||||
"""
|
||||
similar_documents: list = []
|
||||
self.document_store.return_embedding = True # type: ignore
|
||||
|
||||
for document in self.document_store.get_documents_by_id(ids=document_ids, index=index):
|
||||
similar_documents.append(
|
||||
self.document_store.query_by_embedding(
|
||||
query_emb=document.embedding, filters=filters, return_embedding=False, top_k=top_k, index=index
|
||||
)
|
||||
documents = self.document_store.get_documents_by_id(ids=document_ids, index=index)
|
||||
query_embs = [doc.embedding for doc in documents]
|
||||
similar_documents = self.document_store.query_by_embedding_batch(
|
||||
query_embs=query_embs, filters=filters, return_embedding=False, top_k=top_k, index=index
|
||||
)
|
||||
|
||||
self.document_store.return_embedding = False # type: ignore
|
||||
|
||||
@ -91,3 +91,14 @@ class TestInMemoryDocumentStore(DocumentStoreBaseTestAbstract):
|
||||
assert "A Foo Document" in docs[0][0].content
|
||||
assert len(docs[1]) == 5
|
||||
assert "A Bar Document" in docs[1][0].content
|
||||
|
||||
@pytest.mark.integration
|
||||
def test_memory_query_by_embedding_batch(self, ds, documents):
|
||||
documents = [doc for doc in documents if doc.embedding is not None]
|
||||
ds.write_documents(documents)
|
||||
query_embs = [doc.embedding for doc in documents]
|
||||
docs_batch = ds.query_by_embedding_batch(query_embs=query_embs, top_k=5)
|
||||
assert len(docs_batch) == 6
|
||||
for docs, query_emb in zip(docs_batch, query_embs):
|
||||
assert len(docs) == 5
|
||||
assert (docs[0].embedding == query_emb).all()
|
||||
|
||||
@ -178,6 +178,20 @@ class TestOpenSearchDocumentStore(DocumentStoreBaseTestAbstract, SearchEngineDoc
|
||||
)
|
||||
assert len(results) == 3
|
||||
|
||||
@pytest.mark.integration
|
||||
@pytest.mark.parametrize("use_ann", [True, False])
|
||||
def test_query_embedding_batch_with_filters(self, ds: OpenSearchDocumentStore, documents, use_ann):
|
||||
ds.embeddings_field_supports_similarity = use_ann
|
||||
ds.write_documents(documents)
|
||||
results = ds.query_by_embedding_batch(
|
||||
query_embs=[np.random.rand(768).astype(np.float32) for _ in range(2)],
|
||||
filters=[{"year": "2020"} for _ in range(2)],
|
||||
top_k=10,
|
||||
)
|
||||
assert len(results) == 2
|
||||
for result in results:
|
||||
assert len(result) == 3
|
||||
|
||||
# Unit tests
|
||||
|
||||
@pytest.mark.unit
|
||||
@ -321,6 +335,13 @@ class TestOpenSearchDocumentStore(DocumentStoreBaseTestAbstract, SearchEngineDoc
|
||||
_, kwargs = mocked_document_store.client.search.call_args
|
||||
assert kwargs["body"]["_source"] == {"excludes": ["foo", "embedding"]}
|
||||
|
||||
@pytest.mark.unit
|
||||
def test_query_by_embedding_batch_uses_msearch(self, mocked_document_store):
|
||||
mocked_document_store.query_by_embedding_batch([self.query_emb for _ in range(10)])
|
||||
# assert the resulting body is consistent with the `excluded_meta_data` value
|
||||
_, kwargs = mocked_document_store.client.msearch.call_args
|
||||
assert len(kwargs["body"]) == 20 # each search has headers and request
|
||||
|
||||
@pytest.mark.unit
|
||||
def test__create_document_index_with_alias(self, mocked_document_store, caplog):
|
||||
mocked_document_store.client.indices.exists_alias.return_value = True
|
||||
|
||||
@ -809,6 +809,22 @@ def test_multimodal_text_retrieval(text_docs: List[Document]):
|
||||
assert results[0].content == "My name is Christelle and I live in Paris"
|
||||
|
||||
|
||||
@pytest.mark.integration
|
||||
def test_multimodal_text_retrieval_batch(text_docs: List[Document]):
|
||||
retriever = MultiModalRetriever(
|
||||
document_store=InMemoryDocumentStore(return_embedding=True),
|
||||
query_embedding_model="sentence-transformers/multi-qa-mpnet-base-dot-v1",
|
||||
document_embedding_models={"text": "sentence-transformers/multi-qa-mpnet-base-dot-v1"},
|
||||
)
|
||||
retriever.document_store.write_documents(text_docs)
|
||||
retriever.document_store.update_embeddings(retriever=retriever)
|
||||
|
||||
results = retriever.retrieve_batch(queries=["Who lives in Paris?", "Who lives in Berlin?", "Who lives in Madrid?"])
|
||||
assert results[0][0].content == "My name is Christelle and I live in Paris"
|
||||
assert results[1][0].content == "My name is Carla and I live in Berlin"
|
||||
assert results[2][0].content == "My name is Camila and I live in Madrid"
|
||||
|
||||
|
||||
@pytest.mark.integration
|
||||
def test_multimodal_table_retrieval(table_docs: List[Document]):
|
||||
retriever = MultiModalRetriever(
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user