haystack/test/pipelines/test_standard_pipelines.py
Stefano Fiorucci 3040e59c63
feat: add support for BM25Retriever in InMemoryDocumentStore (#3561)
* very first draft

* implement query and query_batch

* add more bm25 parameters

* add rank_bm25 dependency

* fix mypy

* remove tokenizer callable parameter

* remove unused import

* only json serializable attributes

* try to fix: pylint too-many-public-methods / R0904

* bm25 attribute always present

* convert errors into warnings to make the tutorial 1 work

* add docstrings; tests

* try to make tests run

* better docstrings; revert not running tests

* some suggestions from review

* rename elasticsearch retriever as bm25 in tests; try to test memory_bm25

* exclude tests with filters

* change elasticsearch to bm25 retriever in test_summarizer

* add tests

* try to improve tests

* better type hint

* adapt test_table_text_retriever_embedding

* handle non-textual docs

* query only textual documents
2022-11-22 09:24:52 +01:00

537 lines
23 KiB
Python

from pathlib import Path
from collections import defaultdict
from unittest.mock import Mock
import os
import math
import pytest
from haystack.document_stores.elasticsearch import ElasticsearchDocumentStore
from haystack.pipelines import Pipeline, FAQPipeline, DocumentSearchPipeline, RootNode, MostSimilarDocumentsPipeline
from haystack.nodes import (
DensePassageRetriever,
BM25Retriever,
SklearnQueryClassifier,
TransformersQueryClassifier,
EmbeddingRetriever,
JoinDocuments,
)
from haystack.schema import Document
from ..conftest import SAMPLES_PATH
@pytest.mark.parametrize(
"retriever,document_store",
[("embedding", "memory"), ("embedding", "faiss"), ("embedding", "milvus"), ("embedding", "elasticsearch")],
indirect=True,
)
def test_faq_pipeline(retriever, document_store):
documents = [
{"content": "How to test module-1?", "meta": {"source": "wiki1", "answer": "Using tests for module-1"}},
{"content": "How to test module-2?", "meta": {"source": "wiki2", "answer": "Using tests for module-2"}},
{"content": "How to test module-3?", "meta": {"source": "wiki3", "answer": "Using tests for module-3"}},
{"content": "How to test module-4?", "meta": {"source": "wiki4", "answer": "Using tests for module-4"}},
{"content": "How to test module-5?", "meta": {"source": "wiki5", "answer": "Using tests for module-5"}},
]
document_store.write_documents(documents)
document_store.update_embeddings(retriever)
pipeline = FAQPipeline(retriever=retriever)
output = pipeline.run(query="How to test this?", params={"Retriever": {"top_k": 3}})
assert len(output["answers"]) == 3
assert output["query"].startswith("How to")
assert output["answers"][0].answer.startswith("Using tests")
if isinstance(document_store, ElasticsearchDocumentStore):
output = pipeline.run(
query="How to test this?", params={"Retriever": {"filters": {"source": ["wiki2"]}, "top_k": 5}}
)
assert len(output["answers"]) == 1
@pytest.mark.parametrize("retriever,document_store", [("embedding", "memory")], indirect=True)
def test_faq_pipeline_batch(retriever, document_store):
documents = [
{"content": "How to test module-1?", "meta": {"source": "wiki1", "answer": "Using tests for module-1"}},
{"content": "How to test module-2?", "meta": {"source": "wiki2", "answer": "Using tests for module-2"}},
{"content": "How to test module-3?", "meta": {"source": "wiki3", "answer": "Using tests for module-3"}},
{"content": "How to test module-4?", "meta": {"source": "wiki4", "answer": "Using tests for module-4"}},
{"content": "How to test module-5?", "meta": {"source": "wiki5", "answer": "Using tests for module-5"}},
]
document_store.write_documents(documents)
document_store.update_embeddings(retriever)
pipeline = FAQPipeline(retriever=retriever)
output = pipeline.run_batch(queries=["How to test this?", "How to test this?"], params={"Retriever": {"top_k": 3}})
assert len(output["answers"]) == 2 # 2 queries
assert len(output["answers"][0]) == 3 # 3 answers per query
assert output["queries"][0].startswith("How to")
assert output["answers"][0][0].answer.startswith("Using tests")
@pytest.mark.parametrize("retriever", ["embedding"], indirect=True)
@pytest.mark.parametrize(
"document_store", ["elasticsearch", "faiss", "memory", "milvus", "weaviate", "pinecone"], indirect=True
)
def test_document_search_pipeline(retriever, document_store):
documents = [
{"content": "Sample text for document-1", "meta": {"source": "wiki1"}},
{"content": "Sample text for document-2", "meta": {"source": "wiki2"}},
{"content": "Sample text for document-3", "meta": {"source": "wiki3"}},
{"content": "Sample text for document-4", "meta": {"source": "wiki4"}},
{"content": "Sample text for document-5", "meta": {"source": "wiki5"}},
]
document_store.write_documents(documents)
document_store.update_embeddings(retriever)
pipeline = DocumentSearchPipeline(retriever=retriever)
output = pipeline.run(query="How to test this?", params={"top_k": 4})
assert len(output.get("documents", [])) == 4
if isinstance(document_store, ElasticsearchDocumentStore):
output = pipeline.run(query="How to test this?", params={"filters": {"source": ["wiki2"]}, "top_k": 5})
assert len(output["documents"]) == 1
@pytest.mark.parametrize("retriever", ["embedding"], indirect=True)
@pytest.mark.parametrize("document_store", ["memory"], indirect=True)
def test_document_search_pipeline_batch(retriever, document_store):
documents = [
{"content": "Sample text for document-1", "meta": {"source": "wiki1"}},
{"content": "Sample text for document-2", "meta": {"source": "wiki2"}},
{"content": "Sample text for document-3", "meta": {"source": "wiki3"}},
{"content": "Sample text for document-4", "meta": {"source": "wiki4"}},
{"content": "Sample text for document-5", "meta": {"source": "wiki5"}},
]
document_store.write_documents(documents)
document_store.update_embeddings(retriever)
pipeline = DocumentSearchPipeline(retriever=retriever)
output = pipeline.run_batch(queries=["How to test this?", "How to test this?"], params={"top_k": 4})
assert len(output["documents"]) == 2 # 2 queries
assert len(output["documents"][0]) == 4 # 4 docs per query
@pytest.mark.integration
@pytest.mark.parametrize("retriever_with_docs", ["bm25", "dpr", "embedding"], indirect=True)
@pytest.mark.parametrize("document_store_with_docs", ["elasticsearch"], indirect=True)
def test_documentsearch_es_authentication(retriever_with_docs, document_store_with_docs: ElasticsearchDocumentStore):
if isinstance(retriever_with_docs, (DensePassageRetriever, EmbeddingRetriever)):
document_store_with_docs.update_embeddings(retriever=retriever_with_docs)
mock_client = Mock(wraps=document_store_with_docs.client)
document_store_with_docs.client = mock_client
auth_headers = {"Authorization": "Basic YWRtaW46cm9vdA=="}
pipeline = DocumentSearchPipeline(retriever=retriever_with_docs)
prediction = pipeline.run(
query="Who lives in Berlin?", params={"Retriever": {"top_k": 10, "headers": auth_headers}}
)
assert prediction is not None
assert len(prediction["documents"]) == 5
mock_client.search.assert_called_once()
args, kwargs = mock_client.search.call_args
assert "headers" in kwargs
assert kwargs["headers"] == auth_headers
@pytest.mark.integration
@pytest.mark.parametrize("retriever_with_docs", ["tfidf"], indirect=True)
def test_documentsearch_document_store_authentication(retriever_with_docs, document_store_with_docs):
mock_client = None
if isinstance(document_store_with_docs, ElasticsearchDocumentStore):
es_document_store: ElasticsearchDocumentStore = document_store_with_docs
mock_client = Mock(wraps=es_document_store.client)
es_document_store.client = mock_client
auth_headers = {"Authorization": "Basic YWRtaW46cm9vdA=="}
pipeline = DocumentSearchPipeline(retriever=retriever_with_docs)
if not mock_client:
with pytest.raises(Exception):
prediction = pipeline.run(
query="Who lives in Berlin?", params={"Retriever": {"top_k": 10, "headers": auth_headers}}
)
else:
prediction = pipeline.run(
query="Who lives in Berlin?", params={"Retriever": {"top_k": 10, "headers": auth_headers}}
)
assert prediction is not None
assert len(prediction["documents"]) == 5
mock_client.count.assert_called_once()
args, kwargs = mock_client.count.call_args
assert "headers" in kwargs
assert kwargs["headers"] == auth_headers
@pytest.mark.parametrize(
"retriever,document_store",
[("embedding", "faiss"), ("embedding", "milvus"), ("embedding", "elasticsearch")],
indirect=True,
)
def test_most_similar_documents_pipeline(retriever, document_store):
documents = [
{"id": "a", "content": "Sample text for document-1", "meta": {"source": "wiki1"}},
{"id": "b", "content": "Sample text for document-2", "meta": {"source": "wiki2"}},
{"content": "Sample text for document-3", "meta": {"source": "wiki3"}},
{"content": "Sample text for document-4", "meta": {"source": "wiki4"}},
{"content": "Sample text for document-5", "meta": {"source": "wiki5"}},
]
document_store.write_documents(documents)
document_store.update_embeddings(retriever)
docs_id: list = ["a", "b"]
pipeline = MostSimilarDocumentsPipeline(document_store=document_store)
list_of_documents = pipeline.run(document_ids=docs_id)
assert len(list_of_documents[0]) > 1
assert isinstance(list_of_documents, list)
assert len(list_of_documents) == len(docs_id)
for another_list in list_of_documents:
assert isinstance(another_list, list)
for document in another_list:
assert isinstance(document, Document)
assert isinstance(document.id, str)
assert isinstance(document.content, str)
@pytest.mark.parametrize(
"retriever,document_store", [("embedding", "milvus"), ("embedding", "elasticsearch")], indirect=True
)
def test_most_similar_documents_pipeline_with_filters(retriever, document_store):
documents = [
{"id": "a", "content": "Sample text for document-1", "meta": {"source": "wiki1"}},
{"id": "b", "content": "Sample text for document-2", "meta": {"source": "wiki2"}},
{"content": "Sample text for document-3", "meta": {"source": "wiki3"}},
{"content": "Sample text for document-4", "meta": {"source": "wiki4"}},
{"content": "Sample text for document-5", "meta": {"source": "wiki5"}},
]
document_store.write_documents(documents)
document_store.update_embeddings(retriever)
docs_id: list = ["a", "b"]
filters = {"source": ["wiki3", "wiki4", "wiki5"]}
pipeline = MostSimilarDocumentsPipeline(document_store=document_store)
list_of_documents = pipeline.run(document_ids=docs_id, filters=filters)
assert len(list_of_documents[0]) > 1
assert isinstance(list_of_documents, list)
assert len(list_of_documents) == len(docs_id)
for another_list in list_of_documents:
assert isinstance(another_list, list)
for document in another_list:
assert isinstance(document, Document)
assert isinstance(document.id, str)
assert isinstance(document.content, str)
assert document.meta["source"] in ["wiki3", "wiki4", "wiki5"]
@pytest.mark.parametrize("retriever,document_store", [("embedding", "memory")], indirect=True)
def test_most_similar_documents_pipeline_batch(retriever, document_store):
documents = [
{"id": "a", "content": "Sample text for document-1", "meta": {"source": "wiki1"}},
{"id": "b", "content": "Sample text for document-2", "meta": {"source": "wiki2"}},
{"content": "Sample text for document-3", "meta": {"source": "wiki3"}},
{"content": "Sample text for document-4", "meta": {"source": "wiki4"}},
{"content": "Sample text for document-5", "meta": {"source": "wiki5"}},
]
document_store.write_documents(documents)
document_store.update_embeddings(retriever)
docs_id: list = ["a", "b"]
pipeline = MostSimilarDocumentsPipeline(document_store=document_store)
list_of_documents = pipeline.run_batch(document_ids=docs_id)
assert len(list_of_documents[0]) > 1
assert isinstance(list_of_documents, list)
assert len(list_of_documents) == len(docs_id)
for another_list in list_of_documents:
assert isinstance(another_list, list)
for document in another_list:
assert isinstance(document, Document)
assert isinstance(document.id, str)
assert isinstance(document.content, str)
@pytest.mark.parametrize("retriever,document_store", [("embedding", "memory")], indirect=True)
def test_most_similar_documents_pipeline_with_filters_batch(retriever, document_store):
documents = [
{"id": "a", "content": "Sample text for document-1", "meta": {"source": "wiki1"}},
{"id": "b", "content": "Sample text for document-2", "meta": {"source": "wiki2"}},
{"content": "Sample text for document-3", "meta": {"source": "wiki3"}},
{"content": "Sample text for document-4", "meta": {"source": "wiki4"}},
{"content": "Sample text for document-5", "meta": {"source": "wiki5"}},
]
document_store.write_documents(documents)
document_store.update_embeddings(retriever)
docs_id: list = ["a", "b"]
filters = {"source": ["wiki3", "wiki4", "wiki5"]}
pipeline = MostSimilarDocumentsPipeline(document_store=document_store)
list_of_documents = pipeline.run_batch(document_ids=docs_id, filters=filters)
assert len(list_of_documents[0]) > 1
assert isinstance(list_of_documents, list)
assert len(list_of_documents) == len(docs_id)
for another_list in list_of_documents:
assert isinstance(another_list, list)
for document in another_list:
assert isinstance(document, Document)
assert isinstance(document.id, str)
assert isinstance(document.content, str)
assert document.meta["source"] in ["wiki3", "wiki4", "wiki5"]
@pytest.mark.elasticsearch
@pytest.mark.parametrize("document_store_dot_product_with_docs", ["elasticsearch"], indirect=True)
def test_join_merge_no_weights(document_store_dot_product_with_docs):
es = BM25Retriever(document_store=document_store_dot_product_with_docs)
dpr = DensePassageRetriever(
document_store=document_store_dot_product_with_docs,
query_embedding_model="facebook/dpr-question_encoder-single-nq-base",
passage_embedding_model="facebook/dpr-ctx_encoder-single-nq-base",
use_gpu=False,
)
document_store_dot_product_with_docs.update_embeddings(dpr)
query = "Where does Carla live?"
join_node = JoinDocuments(join_mode="merge")
p = Pipeline()
p.add_node(component=es, name="R1", inputs=["Query"])
p.add_node(component=dpr, name="R2", inputs=["Query"])
p.add_node(component=join_node, name="Join", inputs=["R1", "R2"])
results = p.run(query=query)
assert len(results["documents"]) == 5
@pytest.mark.elasticsearch
@pytest.mark.parametrize("document_store_dot_product_with_docs", ["elasticsearch"], indirect=True)
def test_join_merge_with_weights(document_store_dot_product_with_docs):
es = BM25Retriever(document_store=document_store_dot_product_with_docs)
dpr = DensePassageRetriever(
document_store=document_store_dot_product_with_docs,
query_embedding_model="facebook/dpr-question_encoder-single-nq-base",
passage_embedding_model="facebook/dpr-ctx_encoder-single-nq-base",
use_gpu=False,
)
document_store_dot_product_with_docs.update_embeddings(dpr)
query = "Where does Carla live?"
join_node = JoinDocuments(join_mode="merge", weights=[1000, 1], top_k_join=2)
p = Pipeline()
p.add_node(component=es, name="R1", inputs=["Query"])
p.add_node(component=dpr, name="R2", inputs=["Query"])
p.add_node(component=join_node, name="Join", inputs=["R1", "R2"])
results = p.run(query=query)
assert math.isclose(results["documents"][0].score, 0.5481393431183286, rel_tol=0.0001)
assert len(results["documents"]) == 2
@pytest.mark.elasticsearch
@pytest.mark.parametrize("document_store_dot_product_with_docs", ["elasticsearch"], indirect=True)
def test_join_concatenate(document_store_dot_product_with_docs):
es = BM25Retriever(document_store=document_store_dot_product_with_docs)
dpr = DensePassageRetriever(
document_store=document_store_dot_product_with_docs,
query_embedding_model="facebook/dpr-question_encoder-single-nq-base",
passage_embedding_model="facebook/dpr-ctx_encoder-single-nq-base",
use_gpu=False,
)
document_store_dot_product_with_docs.update_embeddings(dpr)
query = "Where does Carla live?"
join_node = JoinDocuments(join_mode="concatenate")
p = Pipeline()
p.add_node(component=es, name="R1", inputs=["Query"])
p.add_node(component=dpr, name="R2", inputs=["Query"])
p.add_node(component=join_node, name="Join", inputs=["R1", "R2"])
results = p.run(query=query)
assert len(results["documents"]) == 5
@pytest.mark.elasticsearch
@pytest.mark.parametrize("document_store_dot_product_with_docs", ["elasticsearch"], indirect=True)
def test_join_concatenate_with_topk(document_store_dot_product_with_docs):
es = BM25Retriever(document_store=document_store_dot_product_with_docs)
dpr = DensePassageRetriever(
document_store=document_store_dot_product_with_docs,
query_embedding_model="facebook/dpr-question_encoder-single-nq-base",
passage_embedding_model="facebook/dpr-ctx_encoder-single-nq-base",
use_gpu=False,
)
document_store_dot_product_with_docs.update_embeddings(dpr)
query = "Where does Carla live?"
join_node = JoinDocuments(join_mode="concatenate")
p = Pipeline()
p.add_node(component=es, name="R1", inputs=["Query"])
p.add_node(component=dpr, name="R2", inputs=["Query"])
p.add_node(component=join_node, name="Join", inputs=["R1", "R2"])
one_result = p.run(query=query, params={"Join": {"top_k_join": 1}})
two_results = p.run(query=query, params={"Join": {"top_k_join": 2}})
assert len(one_result["documents"]) == 1
assert len(two_results["documents"]) == 2
@pytest.mark.elasticsearch
@pytest.mark.parametrize("document_store_dot_product_with_docs", ["elasticsearch"], indirect=True)
@pytest.mark.parametrize("reader", ["farm"], indirect=True)
def test_join_with_reader(document_store_dot_product_with_docs, reader):
es = BM25Retriever(document_store=document_store_dot_product_with_docs)
dpr = DensePassageRetriever(
document_store=document_store_dot_product_with_docs,
query_embedding_model="facebook/dpr-question_encoder-single-nq-base",
passage_embedding_model="facebook/dpr-ctx_encoder-single-nq-base",
use_gpu=False,
)
document_store_dot_product_with_docs.update_embeddings(dpr)
query = "Where does Carla live?"
join_node = JoinDocuments()
p = Pipeline()
p.add_node(component=es, name="R1", inputs=["Query"])
p.add_node(component=dpr, name="R2", inputs=["Query"])
p.add_node(component=join_node, name="Join", inputs=["R1", "R2"])
p.add_node(component=reader, name="Reader", inputs=["Join"])
results = p.run(query=query)
# check whether correct answer is within top 2 predictions
assert results["answers"][0].answer == "Berlin" or results["answers"][1].answer == "Berlin"
@pytest.mark.elasticsearch
@pytest.mark.parametrize("document_store_dot_product_with_docs", ["elasticsearch"], indirect=True)
def test_join_with_rrf(document_store_dot_product_with_docs):
es = BM25Retriever(document_store=document_store_dot_product_with_docs)
dpr = DensePassageRetriever(
document_store=document_store_dot_product_with_docs,
query_embedding_model="facebook/dpr-question_encoder-single-nq-base",
passage_embedding_model="facebook/dpr-ctx_encoder-single-nq-base",
use_gpu=False,
)
document_store_dot_product_with_docs.update_embeddings(dpr)
query = "Where does Carla live?"
join_node = JoinDocuments(join_mode="reciprocal_rank_fusion")
p = Pipeline()
p.add_node(component=es, name="R1", inputs=["Query"])
p.add_node(component=dpr, name="R2", inputs=["Query"])
p.add_node(component=join_node, name="Join", inputs=["R1", "R2"])
results = p.run(query=query)
# list of precalculated expected results
expected_scores = [
0.03278688524590164,
0.03200204813108039,
0.03200204813108039,
0.031009615384615385,
0.031009615384615385,
]
assert all([doc.score == expected_scores[idx] for idx, doc in enumerate(results["documents"])])
def test_query_keyword_statement_classifier():
class KeywordOutput(RootNode):
outgoing_edges = 2
def run(self, **kwargs):
kwargs["output"] = "keyword"
return kwargs, "output_1"
class QuestionOutput(RootNode):
outgoing_edges = 2
def run(self, **kwargs):
kwargs["output"] = "question"
return kwargs, "output_2"
pipeline = Pipeline()
pipeline.add_node(name="SkQueryKeywordQuestionClassifier", component=SklearnQueryClassifier(), inputs=["Query"])
pipeline.add_node(
name="KeywordNode", component=KeywordOutput(), inputs=["SkQueryKeywordQuestionClassifier.output_2"]
)
pipeline.add_node(
name="QuestionNode", component=QuestionOutput(), inputs=["SkQueryKeywordQuestionClassifier.output_1"]
)
output = pipeline.run(query="morse code")
assert output["output"] == "keyword"
output = pipeline.run(query="How old is John?")
assert output["output"] == "question"
pipeline = Pipeline()
pipeline.add_node(
name="TfQueryKeywordQuestionClassifier", component=TransformersQueryClassifier(), inputs=["Query"]
)
pipeline.add_node(
name="KeywordNode", component=KeywordOutput(), inputs=["TfQueryKeywordQuestionClassifier.output_2"]
)
pipeline.add_node(
name="QuestionNode", component=QuestionOutput(), inputs=["TfQueryKeywordQuestionClassifier.output_1"]
)
output = pipeline.run(query="morse code")
assert output["output"] == "keyword"
output = pipeline.run(query="How old is John?")
assert output["output"] == "question"
@pytest.mark.elasticsearch
@pytest.mark.parametrize("document_store", ["elasticsearch"], indirect=True)
def test_indexing_pipeline_with_classifier(document_store):
# test correct load of indexing pipeline from yaml
pipeline = Pipeline.load_from_yaml(
SAMPLES_PATH / "pipeline" / "test.haystack-pipeline.yml", pipeline_name="indexing_pipeline_with_classifier"
)
pipeline.run(file_paths=SAMPLES_PATH / "pdf" / "sample_pdf_1.pdf")
# test correct load of query pipeline from yaml
pipeline = Pipeline.load_from_yaml(
SAMPLES_PATH / "pipeline" / "test.haystack-pipeline.yml", pipeline_name="query_pipeline"
)
prediction = pipeline.run(
query="Who made the PDF specification?", params={"ESRetriever": {"top_k": 10}, "Reader": {"top_k": 3}}
)
assert prediction["query"] == "Who made the PDF specification?"
assert prediction["answers"][0].answer == "Adobe Systems"
assert prediction["answers"][0].meta["classification"]["label"] == "joy"
assert "_debug" not in prediction.keys()
@pytest.mark.elasticsearch
@pytest.mark.parametrize("document_store", ["elasticsearch"], indirect=True)
def test_query_pipeline_with_document_classifier(document_store):
# test correct load of indexing pipeline from yaml
pipeline = Pipeline.load_from_yaml(
SAMPLES_PATH / "pipeline" / "test.haystack-pipeline.yml", pipeline_name="indexing_pipeline"
)
pipeline.run(file_paths=SAMPLES_PATH / "pdf" / "sample_pdf_1.pdf")
# test correct load of query pipeline from yaml
pipeline = Pipeline.load_from_yaml(
SAMPLES_PATH / "pipeline" / "test.haystack-pipeline.yml",
pipeline_name="query_pipeline_with_document_classifier",
)
prediction = pipeline.run(
query="Who made the PDF specification?", params={"ESRetriever": {"top_k": 10}, "Reader": {"top_k": 3}}
)
assert prediction["query"] == "Who made the PDF specification?"
assert prediction["answers"][0].answer == "Adobe Systems"
assert prediction["answers"][0].meta["classification"]["label"] == "joy"
assert "_debug" not in prediction.keys()