haystack/test/test_faiss_and_milvus.py
tstadel 7d6b3fe954
Add flag to disable scaling scores to probabilities (#2454)
* add scale_scores_to_probabilities flag

* Update Documentation & Code Style

* fix tests

* fix sql mypy

* Update Documentation & Code Style

* fix responses

* Update Documentation & Code Style

* rename to scale_score_to_probability + docstrings

* use BaseDocumentStore.score_to_probability in elasticsearch and milvus2

* Update Documentation & Code Style

* fix tests

* Update Documentation & Code Style

* add tests

* improve naming

* Update Documentation & Code Style

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2022-05-02 13:35:07 +02:00

569 lines
24 KiB
Python

import uuid
import faiss
import math
import numpy as np
import pytest
import sys
from haystack.schema import Document
from haystack.pipelines import DocumentSearchPipeline
from haystack.document_stores.faiss import FAISSDocumentStore
from haystack.document_stores.weaviate import WeaviateDocumentStore
from haystack.pipelines import Pipeline
from haystack.nodes.retriever.dense import EmbeddingRetriever
from .conftest import ensure_ids_are_correct_uuids
DOCUMENTS = [
{
"meta": {"name": "name_1", "year": "2020", "month": "01"},
"content": "text_1",
"embedding": np.random.rand(768).astype(np.float32),
},
{
"meta": {"name": "name_2", "year": "2020", "month": "02"},
"content": "text_2",
"embedding": np.random.rand(768).astype(np.float32),
},
{
"meta": {"name": "name_3", "year": "2020", "month": "03"},
"content": "text_3",
"embedding": np.random.rand(768).astype(np.float64),
},
{
"meta": {"name": "name_4", "year": "2021", "month": "01"},
"content": "text_4",
"embedding": np.random.rand(768).astype(np.float32),
},
{
"meta": {"name": "name_5", "year": "2021", "month": "02"},
"content": "text_5",
"embedding": np.random.rand(768).astype(np.float32),
},
{
"meta": {"name": "name_6", "year": "2021", "month": "03"},
"content": "text_6",
"embedding": np.random.rand(768).astype(np.float64),
},
]
@pytest.mark.skipif(sys.platform in ["win32", "cygwin"], reason="Test with tmp_path not working on windows runner")
def test_faiss_index_save_and_load(tmp_path, sql_url):
document_store = FAISSDocumentStore(
sql_url=sql_url,
index="haystack_test",
progress_bar=False, # Just to check if the init parameters are kept
isolation_level="AUTOCOMMIT",
)
document_store.write_documents(DOCUMENTS)
# test saving the index
document_store.save(tmp_path / "haystack_test_faiss")
# clear existing faiss_index
document_store.faiss_indexes[document_store.index].reset()
# test faiss index is cleared
assert document_store.faiss_indexes[document_store.index].ntotal == 0
# test loading the index
new_document_store = FAISSDocumentStore.load(tmp_path / "haystack_test_faiss")
# check faiss index is restored
assert new_document_store.faiss_indexes[document_store.index].ntotal == len(DOCUMENTS)
# check if documents are restored
assert len(new_document_store.get_all_documents()) == len(DOCUMENTS)
# Check if the init parameters are kept
assert not new_document_store.progress_bar
# test saving and loading the loaded faiss index
new_document_store.save(tmp_path / "haystack_test_faiss")
reloaded_document_store = FAISSDocumentStore.load(tmp_path / "haystack_test_faiss")
# check faiss index is restored
assert reloaded_document_store.faiss_indexes[document_store.index].ntotal == len(DOCUMENTS)
# check if documents are restored
assert len(reloaded_document_store.get_all_documents()) == len(DOCUMENTS)
# Check if the init parameters are kept
assert not reloaded_document_store.progress_bar
# test loading the index via init
new_document_store = FAISSDocumentStore(faiss_index_path=tmp_path / "haystack_test_faiss")
# check faiss index is restored
assert new_document_store.faiss_indexes[document_store.index].ntotal == len(DOCUMENTS)
# check if documents are restored
assert len(new_document_store.get_all_documents()) == len(DOCUMENTS)
# Check if the init parameters are kept
assert not new_document_store.progress_bar
@pytest.mark.skipif(sys.platform in ["win32", "cygwin"], reason="Test with tmp_path not working on windows runner")
def test_faiss_index_save_and_load_custom_path(tmp_path, sql_url):
document_store = FAISSDocumentStore(
sql_url=sql_url,
index="haystack_test",
progress_bar=False, # Just to check if the init parameters are kept
isolation_level="AUTOCOMMIT",
)
document_store.write_documents(DOCUMENTS)
# test saving the index
document_store.save(index_path=tmp_path / "haystack_test_faiss", config_path=tmp_path / "custom_path.json")
# clear existing faiss_index
document_store.faiss_indexes[document_store.index].reset()
# test faiss index is cleared
assert document_store.faiss_indexes[document_store.index].ntotal == 0
# test loading the index
new_document_store = FAISSDocumentStore.load(
index_path=tmp_path / "haystack_test_faiss", config_path=tmp_path / "custom_path.json"
)
# check faiss index is restored
assert new_document_store.faiss_indexes[document_store.index].ntotal == len(DOCUMENTS)
# check if documents are restored
assert len(new_document_store.get_all_documents()) == len(DOCUMENTS)
# Check if the init parameters are kept
assert not new_document_store.progress_bar
# test saving and loading the loaded faiss index
new_document_store.save(tmp_path / "haystack_test_faiss", config_path=tmp_path / "custom_path.json")
reloaded_document_store = FAISSDocumentStore.load(
tmp_path / "haystack_test_faiss", config_path=tmp_path / "custom_path.json"
)
# check faiss index is restored
assert reloaded_document_store.faiss_indexes[document_store.index].ntotal == len(DOCUMENTS)
# check if documents are restored
assert len(reloaded_document_store.get_all_documents()) == len(DOCUMENTS)
# Check if the init parameters are kept
assert not reloaded_document_store.progress_bar
# test loading the index via init
new_document_store = FAISSDocumentStore(
faiss_index_path=tmp_path / "haystack_test_faiss", faiss_config_path=tmp_path / "custom_path.json"
)
# check faiss index is restored
assert new_document_store.faiss_indexes[document_store.index].ntotal == len(DOCUMENTS)
# check if documents are restored
assert len(new_document_store.get_all_documents()) == len(DOCUMENTS)
# Check if the init parameters are kept
assert not new_document_store.progress_bar
@pytest.mark.skipif(sys.platform in ["win32", "cygwin"], reason="Test with tmp_path not working on windows runner")
def test_faiss_index_mutual_exclusive_args(tmp_path):
with pytest.raises(ValueError):
FAISSDocumentStore(
sql_url=f"sqlite:////{tmp_path/'haystack_test.db'}",
faiss_index_path=f"{tmp_path/'haystack_test'}",
isolation_level="AUTOCOMMIT",
)
with pytest.raises(ValueError):
FAISSDocumentStore(
f"sqlite:////{tmp_path/'haystack_test.db'}",
faiss_index_path=f"{tmp_path/'haystack_test'}",
isolation_level="AUTOCOMMIT",
)
@pytest.mark.parametrize("document_store", ["faiss"], indirect=True)
@pytest.mark.parametrize("index_buffer_size", [10_000, 2])
@pytest.mark.parametrize("batch_size", [2])
def test_faiss_write_docs(document_store, index_buffer_size, batch_size):
document_store.index_buffer_size = index_buffer_size
# Write in small batches
for i in range(0, len(DOCUMENTS), batch_size):
document_store.write_documents(DOCUMENTS[i : i + batch_size])
documents_indexed = document_store.get_all_documents()
assert len(documents_indexed) == len(DOCUMENTS)
# test if correct vectors are associated with docs
for i, doc in enumerate(documents_indexed):
# we currently don't get the embeddings back when we call document_store.get_all_documents()
original_doc = [d for d in DOCUMENTS if d["content"] == doc.content][0]
stored_emb = document_store.faiss_indexes[document_store.index].reconstruct(int(doc.meta["vector_id"]))
# compare original input vec with stored one (ignore extra dim added by hnsw)
# original input vec is normalized as faiss only stores normalized vectors
assert np.allclose(original_doc["embedding"] / np.linalg.norm(original_doc["embedding"]), stored_emb, rtol=0.01)
@pytest.mark.slow
@pytest.mark.parametrize("retriever", ["dpr"], indirect=True)
@pytest.mark.parametrize("document_store", ["faiss", "milvus1", "milvus"], indirect=True)
@pytest.mark.parametrize("batch_size", [4, 6])
def test_update_docs(document_store, retriever, batch_size):
# initial write
document_store.write_documents(DOCUMENTS)
document_store.update_embeddings(retriever=retriever, batch_size=batch_size)
documents_indexed = document_store.get_all_documents()
assert len(documents_indexed) == len(DOCUMENTS)
# test if correct vectors are associated with docs
for doc in documents_indexed:
original_doc = [d for d in DOCUMENTS if d["content"] == doc.content][0]
updated_embedding = retriever.embed_documents([Document.from_dict(original_doc)])
stored_doc = document_store.get_all_documents(filters={"name": [doc.meta["name"]]})[0]
# compare original input vec with stored one (ignore extra dim added by hnsw)
# original input vec is normalized as faiss only stores normalized vectors
a = updated_embedding / np.linalg.norm(updated_embedding)
assert np.allclose(a[0], stored_doc.embedding, rtol=0.2) # high tolerance necessary for Milvus 2
@pytest.mark.slow
@pytest.mark.parametrize("retriever", ["dpr"], indirect=True)
@pytest.mark.parametrize("document_store", ["milvus1", "milvus", "faiss"], indirect=True)
def test_update_existing_docs(document_store, retriever):
document_store.duplicate_documents = "overwrite"
old_document = Document(content="text_1")
# initial write
document_store.write_documents([old_document])
document_store.update_embeddings(retriever=retriever)
old_documents_indexed = document_store.get_all_documents(return_embedding=True)
assert len(old_documents_indexed) == 1
# Update document data
new_document = Document(content="text_2")
new_document.id = old_document.id
document_store.write_documents([new_document])
document_store.update_embeddings(retriever=retriever)
new_documents_indexed = document_store.get_all_documents(return_embedding=True)
assert len(new_documents_indexed) == 1
assert old_documents_indexed[0].id == new_documents_indexed[0].id
assert old_documents_indexed[0].content == "text_1"
assert new_documents_indexed[0].content == "text_2"
print(type(old_documents_indexed[0].embedding))
print(type(new_documents_indexed[0].embedding))
assert not np.allclose(old_documents_indexed[0].embedding, new_documents_indexed[0].embedding, rtol=0.01)
@pytest.mark.parametrize("retriever", ["dpr"], indirect=True)
@pytest.mark.parametrize("document_store", ["faiss", "milvus1", "milvus"], indirect=True)
def test_update_with_empty_store(document_store, retriever):
# Call update with empty doc store
document_store.update_embeddings(retriever=retriever)
# initial write
document_store.write_documents(DOCUMENTS)
documents_indexed = document_store.get_all_documents()
assert len(documents_indexed) == len(DOCUMENTS)
@pytest.mark.skipif(sys.platform in ["win32", "cygwin"], reason="Test with tmp_path not working on windows runner")
@pytest.mark.parametrize("index_factory", ["Flat", "HNSW", "IVF1,Flat"])
def test_faiss_retrieving(index_factory, tmp_path):
document_store = FAISSDocumentStore(
sql_url=f"sqlite:////{tmp_path/'test_faiss_retrieving.db'}",
faiss_index_factory_str=index_factory,
isolation_level="AUTOCOMMIT",
)
document_store.delete_all_documents(index="document")
if "ivf" in index_factory.lower():
document_store.train_index(DOCUMENTS)
document_store.write_documents(DOCUMENTS)
retriever = EmbeddingRetriever(
document_store=document_store, embedding_model="deepset/sentence_bert", use_gpu=False
)
result = retriever.retrieve(query="How to test this?")
assert len(result) == len(DOCUMENTS)
assert type(result[0]) == Document
# Cleanup
document_store.faiss_indexes[document_store.index].reset()
@pytest.mark.parametrize("retriever", ["embedding"], indirect=True)
@pytest.mark.parametrize("document_store", ["faiss", "milvus1", "milvus"], indirect=True)
def test_finding(document_store, retriever):
document_store.write_documents(DOCUMENTS)
pipe = DocumentSearchPipeline(retriever=retriever)
prediction = pipe.run(query="How to test this?", params={"Retriever": {"top_k": 1}})
assert len(prediction.get("documents", [])) == 1
@pytest.mark.slow
@pytest.mark.parametrize("retriever", ["dpr"], indirect=True)
@pytest.mark.parametrize("document_store", ["faiss", "milvus1", "milvus"], indirect=True)
def test_delete_docs_with_filters(document_store, retriever):
document_store.write_documents(DOCUMENTS)
document_store.update_embeddings(retriever=retriever, batch_size=4)
assert document_store.get_embedding_count() == 6
document_store.delete_documents(filters={"name": ["name_1", "name_2", "name_3", "name_4"]})
documents = document_store.get_all_documents()
assert len(documents) == 2
assert document_store.get_embedding_count() == 2
assert {doc.meta["name"] for doc in documents} == {"name_5", "name_6"}
@pytest.mark.slow
@pytest.mark.parametrize("retriever", ["dpr"], indirect=True)
@pytest.mark.parametrize("document_store", ["faiss", "milvus1", "milvus"], indirect=True)
def test_delete_docs_with_filters(document_store, retriever):
document_store.write_documents(DOCUMENTS)
document_store.update_embeddings(retriever=retriever, batch_size=4)
assert document_store.get_embedding_count() == 6
document_store.delete_documents(filters={"year": ["2020"]})
documents = document_store.get_all_documents()
assert len(documents) == 3
assert document_store.get_embedding_count() == 3
assert all("2021" == doc.meta["year"] for doc in documents)
@pytest.mark.slow
@pytest.mark.parametrize("retriever", ["dpr"], indirect=True)
@pytest.mark.parametrize("document_store", ["faiss", "milvus1", "milvus"], indirect=True)
def test_delete_docs_with_many_filters(document_store, retriever):
document_store.write_documents(DOCUMENTS)
document_store.update_embeddings(retriever=retriever, batch_size=4)
assert document_store.get_embedding_count() == 6
document_store.delete_documents(filters={"month": ["01"], "year": ["2020"]})
documents = document_store.get_all_documents()
assert len(documents) == 5
assert document_store.get_embedding_count() == 5
assert "name_1" not in {doc.meta["name"] for doc in documents}
@pytest.mark.slow
@pytest.mark.parametrize("retriever", ["dpr"], indirect=True)
@pytest.mark.parametrize("document_store", ["faiss", "milvus1", "milvus"], indirect=True)
def test_delete_docs_by_id(document_store, retriever):
document_store.write_documents(DOCUMENTS)
document_store.update_embeddings(retriever=retriever, batch_size=4)
assert document_store.get_embedding_count() == 6
doc_ids = [doc.id for doc in document_store.get_all_documents()]
ids_to_delete = doc_ids[0:3]
document_store.delete_documents(ids=ids_to_delete)
documents = document_store.get_all_documents()
assert len(documents) == len(doc_ids) - len(ids_to_delete)
assert document_store.get_embedding_count() == len(doc_ids) - len(ids_to_delete)
remaining_ids = [doc.id for doc in documents]
assert all(doc_id not in remaining_ids for doc_id in ids_to_delete)
@pytest.mark.slow
@pytest.mark.parametrize("retriever", ["dpr"], indirect=True)
@pytest.mark.parametrize("document_store", ["faiss", "milvus1", "milvus"], indirect=True)
def test_delete_docs_by_id_with_filters(document_store, retriever):
document_store.write_documents(DOCUMENTS)
document_store.update_embeddings(retriever=retriever, batch_size=4)
assert document_store.get_embedding_count() == 6
ids_to_delete = [doc.id for doc in document_store.get_all_documents(filters={"name": ["name_1", "name_2"]})]
ids_not_to_delete = [
doc.id for doc in document_store.get_all_documents(filters={"name": ["name_3", "name_4", "name_5", "name_6"]})
]
document_store.delete_documents(ids=ids_to_delete, filters={"name": ["name_1", "name_2", "name_3", "name_4"]})
documents = document_store.get_all_documents()
assert len(documents) == len(DOCUMENTS) - len(ids_to_delete)
assert document_store.get_embedding_count() == len(DOCUMENTS) - len(ids_to_delete)
assert all(doc.meta["name"] != "name_1" for doc in documents)
assert all(doc.meta["name"] != "name_2" for doc in documents)
all_ids_left = [doc.id for doc in documents]
assert all(doc_id in all_ids_left for doc_id in ids_not_to_delete)
@pytest.mark.slow
@pytest.mark.parametrize("retriever", ["dpr"], indirect=True)
@pytest.mark.parametrize("document_store", ["faiss", "milvus1", "milvus"], indirect=True)
def test_get_docs_with_filters_one_value(document_store, retriever):
document_store.write_documents(DOCUMENTS)
document_store.update_embeddings(retriever=retriever, batch_size=4)
assert document_store.get_embedding_count() == 6
documents = document_store.get_all_documents(filters={"year": ["2020"]})
assert len(documents) == 3
assert all("2020" == doc.meta["year"] for doc in documents)
@pytest.mark.slow
@pytest.mark.parametrize("retriever", ["dpr"], indirect=True)
@pytest.mark.parametrize("document_store", ["faiss", "milvus1", "milvus"], indirect=True)
def test_get_docs_with_filters_many_values(document_store, retriever):
document_store.write_documents(DOCUMENTS)
document_store.update_embeddings(retriever=retriever, batch_size=4)
assert document_store.get_embedding_count() == 6
documents = document_store.get_all_documents(filters={"name": ["name_5", "name_6"]})
assert len(documents) == 2
assert {doc.meta["name"] for doc in documents} == {"name_5", "name_6"}
@pytest.mark.slow
@pytest.mark.parametrize("retriever", ["dpr"], indirect=True)
@pytest.mark.parametrize("document_store", ["faiss", "milvus1", "milvus"], indirect=True)
def test_get_docs_with_many_filters(document_store, retriever):
document_store.write_documents(DOCUMENTS)
document_store.update_embeddings(retriever=retriever, batch_size=4)
assert document_store.get_embedding_count() == 6
documents = document_store.get_all_documents(filters={"month": ["01"], "year": ["2020"]})
assert len(documents) == 1
assert "name_1" == documents[0].meta["name"]
assert "01" == documents[0].meta["month"]
assert "2020" == documents[0].meta["year"]
@pytest.mark.parametrize("retriever", ["embedding"], indirect=True)
@pytest.mark.parametrize("document_store", ["faiss", "milvus1", "milvus"], indirect=True)
def test_pipeline(document_store, retriever):
documents = [
{"name": "name_1", "content": "text_1", "embedding": np.random.rand(768).astype(np.float32)},
{"name": "name_2", "content": "text_2", "embedding": np.random.rand(768).astype(np.float32)},
{"name": "name_3", "content": "text_3", "embedding": np.random.rand(768).astype(np.float64)},
{"name": "name_4", "content": "text_4", "embedding": np.random.rand(768).astype(np.float32)},
]
document_store.write_documents(documents)
pipeline = Pipeline()
pipeline.add_node(component=retriever, name="FAISS", inputs=["Query"])
output = pipeline.run(query="How to test this?", params={"FAISS": {"top_k": 3}})
assert len(output["documents"]) == 3
@pytest.mark.skipif(sys.platform in ["win32", "cygwin"], reason="Test with tmp_path not working on windows runner")
def test_faiss_passing_index_from_outside(tmp_path):
d = 768
nlist = 2
quantizer = faiss.IndexFlatIP(d)
index = "haystack_test_1"
faiss_index = faiss.IndexIVFFlat(quantizer, d, nlist, faiss.METRIC_INNER_PRODUCT)
faiss_index.set_direct_map_type(faiss.DirectMap.Hashtable)
faiss_index.nprobe = 2
document_store = FAISSDocumentStore(
sql_url=f"sqlite:////{tmp_path/'haystack_test_faiss.db'}",
faiss_index=faiss_index,
index=index,
isolation_level="AUTOCOMMIT",
)
document_store.delete_documents()
# as it is a IVF index we need to train it before adding docs
document_store.train_index(DOCUMENTS)
document_store.write_documents(documents=DOCUMENTS)
documents_indexed = document_store.get_all_documents()
# test if vectors ids are associated with docs
for doc in documents_indexed:
assert 0 <= int(doc.meta["vector_id"]) <= 7
@pytest.mark.parametrize("document_store", ["faiss", "milvus1", "milvus", "weaviate"], indirect=True)
def test_cosine_similarity(document_store):
# below we will write documents to the store and then query it to see if vectors were normalized
ensure_ids_are_correct_uuids(docs=DOCUMENTS, document_store=document_store)
document_store.write_documents(documents=DOCUMENTS)
# note that the same query will be used later when querying after updating the embeddings
query = np.random.rand(768).astype(np.float32)
query_results = document_store.query_by_embedding(query_emb=query, top_k=len(DOCUMENTS), return_embedding=True)
# check if search with cosine similarity returns the correct number of results
assert len(query_results) == len(DOCUMENTS)
indexed_docs = {}
for doc in DOCUMENTS:
indexed_docs[doc["content"]] = doc["embedding"]
indexed_docs[doc["content"]] /= np.linalg.norm(doc["embedding"])
for doc in query_results:
result_emb = doc.embedding
original_emb = indexed_docs[doc.content].astype("float32")
# check if the stored embedding was normalized
np.testing.assert_allclose(
original_emb, result_emb, rtol=0.2, atol=5e-07
) # high tolerance necessary for Milvus 2
# check if the score is plausible for cosine similarity
assert 0 <= doc.score <= 1.0
# now check if vectors are normalized when updating embeddings
class MockRetriever:
def embed_documents(self, docs):
return [np.random.rand(768).astype(np.float32) for doc in docs]
retriever = MockRetriever()
document_store.update_embeddings(retriever=retriever)
query_results = document_store.query_by_embedding(query_emb=query, top_k=len(DOCUMENTS), return_embedding=True)
for doc in query_results:
original_emb = np.array([indexed_docs[doc.content]], dtype="float32")
document_store.normalize_embedding(original_emb[0])
# check if the original embedding has changed after updating the embeddings
assert not np.allclose(original_emb[0], doc.embedding, rtol=0.01)
@pytest.mark.parametrize("document_store_dot_product_small", ["faiss", "milvus1", "milvus"], indirect=True)
def test_normalize_embeddings_diff_shapes(document_store_dot_product_small):
VEC_1 = np.array([0.1, 0.2, 0.3], dtype="float32")
document_store_dot_product_small.normalize_embedding(VEC_1)
assert np.linalg.norm(VEC_1) - 1 < 0.01
VEC_1 = np.array([0.1, 0.2, 0.3], dtype="float32").reshape(1, -1)
document_store_dot_product_small.normalize_embedding(VEC_1)
assert np.linalg.norm(VEC_1) - 1 < 0.01
@pytest.mark.parametrize("document_store_small", ["faiss", "milvus1", "milvus", "weaviate"], indirect=True)
def test_cosine_sanity_check(document_store_small):
VEC_1 = np.array([0.1, 0.2, 0.3], dtype="float32")
VEC_2 = np.array([0.4, 0.5, 0.6], dtype="float32")
# This is the cosine similarity of VEC_1 and VEC_2 calculated using sklearn.metrics.pairwise.cosine_similarity
# The score is normalized to yield a value between 0 and 1.
KNOWN_COSINE = 0.9746317
KNOWN_SCALED_COSINE = (KNOWN_COSINE + 1) / 2
docs = [{"name": "vec_1", "text": "vec_1", "content": "vec_1", "embedding": VEC_1}]
ensure_ids_are_correct_uuids(docs=docs, document_store=document_store_small)
document_store_small.write_documents(documents=docs)
query_results = document_store_small.query_by_embedding(
query_emb=VEC_2, top_k=1, return_embedding=True, scale_score=True
)
# check if faiss returns the same cosine similarity. Manual testing with faiss yielded 0.9746318
assert math.isclose(query_results[0].score, KNOWN_SCALED_COSINE, abs_tol=0.00002)
query_results = document_store_small.query_by_embedding(
query_emb=VEC_2, top_k=1, return_embedding=True, scale_score=False
)
# check if faiss returns the same cosine similarity. Manual testing with faiss yielded 0.9746318
assert math.isclose(query_results[0].score, KNOWN_COSINE, abs_tol=0.00002)