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test_optimize.py
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411 lines (336 loc) · 12.9 KB
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# SPDX-License-Identifier: Apache-2.0
# SPDX-FileCopyrightText: Copyright The Lance Authors
import pickle
import random
import re
import threading
from pathlib import Path
import lance
import numpy as np
import pyarrow as pa
from lance.lance import Compaction
from lance.optimize import RewriteResult
from lance.vector import vec_to_table
def test_dataset_optimize(tmp_path: Path):
base_dir = tmp_path / "dataset"
data = pa.table({"a": range(1000), "b": range(1000)})
dataset = lance.write_dataset(data, base_dir, max_rows_per_file=100)
assert dataset.version == 1
assert len(dataset.get_fragments()) == 10
metrics = dataset.optimize.compact_files(
target_rows_per_fragment=1000,
materialize_deletions=False,
num_threads=1,
)
assert metrics.fragments_removed == 10
assert metrics.fragments_added == 1
assert metrics.files_removed == 10
assert metrics.files_added == 1
assert dataset.version == 3
def test_blob_compaction(tmp_path: Path):
base_dir = tmp_path / "blob_dataset"
blob_field = pa.field(
"blob", pa.large_binary(), metadata={"lance-encoding:blob": "true"}
)
schema = pa.schema([pa.field("id", pa.int32()), blob_field])
blobs = [b"\x01\x02", b"\x03\x04\x05"]
table = pa.table(
{
"id": pa.array([0, 1], type=pa.int32()),
"blob": pa.array(blobs, type=pa.large_binary()),
},
schema=schema,
)
dataset = lance.write_dataset(
table,
base_dir,
schema=schema,
max_rows_per_file=1,
data_storage_version="stable",
)
assert len(dataset.get_fragments()) == 2
dataset.optimize.compact_files(num_threads=1)
assert len(dataset.get_fragments()) == 1
blob_files = dataset.take_blobs("blob", indices=[0, 1])
contents = [blob_files[0].readall(), blob_files[1].readall()]
assert contents == blobs
def test_optimize_max_bytes(tmp_path: Path):
base_dir = tmp_path / "dataset"
arr = pa.array(range(4 * 1024 * 1024))
arr = pa.FixedSizeListArray.from_arrays(arr, 1024)
data = pa.table({"a": arr})
dataset = lance.write_dataset(
data, base_dir, max_rows_per_file=2 * 1024, data_storage_version="stable"
)
assert len(dataset.get_fragments()) == 2
# max_bytes_per_file is too small and we get tiny files
metrics = dataset.optimize.compact_files(
target_rows_per_fragment=100 * 1024,
materialize_deletions=False,
max_bytes_per_file=1000,
batch_size=128,
)
# We get 4 fragments here because we don't actually write any data to the file
# until we've accumulated 8MiB for a page.
assert metrics.fragments_removed == 2
assert metrics.fragments_added == 4
assert metrics.files_removed == 2
assert metrics.files_added == 4
num_frags = len(dataset.get_fragments())
assert num_frags == 4
dataset = lance.write_dataset(
data,
base_dir,
max_rows_per_file=2 * 1024,
data_storage_version="stable",
mode="overwrite",
)
# Same test but use Compaction.plan
plan = Compaction.plan(
dataset,
options=dict(
target_rows_per_fragment=100 * 1024, max_bytes_per_file=1000, batch_size=128
),
)
results = [task.execute(dataset) for task in plan.tasks]
metrics = Compaction.commit(dataset, results)
assert metrics.fragments_removed == 2
assert metrics.fragments_added == 4
assert metrics.files_removed == 2
assert metrics.files_added == 4
dataset = lance.write_dataset(
data,
base_dir,
max_rows_per_file=2 * 1024,
data_storage_version="stable",
mode="overwrite",
)
# In this test max_bytes_per_file is still too small but the batch size
# is so large we read the entire input in a single batch
metrics = dataset.optimize.compact_files(
target_rows_per_fragment=100 * 1024,
materialize_deletions=False,
max_bytes_per_file=1000,
batch_size=2 * 1024,
)
assert metrics.fragments_removed == 2
assert metrics.fragments_added == 2
assert metrics.files_removed == 2
assert metrics.files_added == 2
num_frags = len(dataset.get_fragments())
assert num_frags == 2
def create_table(min, max, nvec, ndim=8):
mat = np.random.uniform(min, max, (nvec, ndim))
tbl = vec_to_table(data=mat)
# Add id column for filtering
tbl = pa.Table.from_pydict(
{
"vector": tbl.column(0).chunk(0),
"id": np.arange(0, nvec),
}
)
return tbl
def test_compact_with_write(tmp_path: Path):
# This test creates a dataset with a manifest containing fragments
# that are not in sorted order (by id)
#
# We do this by running compaction concurrently with append
#
# This is because compaction first reserves a fragment id. Then the
# concurrent writes grab later ids and commit them. Then the compaction
# commits with its earlier id.
#
# In the next compaction we should detect this, and reorder the fragments
# when writing the compacted file.
base_dir = tmp_path / "dataset"
NUM_FRAGS = 5
ROWS_PER_FRAG = 300
# First, create some data
data = create_table(min=0, max=1, nvec=ROWS_PER_FRAG)
dataset = lance.write_dataset(data, base_dir)
for _ in range(NUM_FRAGS):
lance.write_dataset(data, base_dir, mode="append")
# Now, run compaction at the same time as creating new data
def do_compaction():
dataset = lance.dataset(base_dir)
dataset.optimize.compact_files()
compact_thread = threading.Thread(target=do_compaction)
compact_thread.start()
for _ in range(NUM_FRAGS):
lance.write_dataset(data, base_dir, mode="append")
compact_thread.join()
# Now, run compaction again, this should succeed
dataset = lance.dataset(base_dir)
dataset.optimize.compact_files()
assert dataset.to_table().num_rows == ROWS_PER_FRAG * (NUM_FRAGS * 2 + 1)
def test_index_remapping(tmp_path: Path):
base_dir = tmp_path / "dataset"
data = create_table(min=0, max=1, nvec=300)
dataset = lance.write_dataset(data, base_dir, max_rows_per_file=150)
dataset.create_index(
"vector", index_type="IVF_PQ", num_partitions=2, num_sub_vectors=2
)
assert len(dataset.get_fragments()) == 2
sample_query_indices = random.sample(range(300), 50)
vecs = data.column("vector").chunk(0)
sample_queries = [
{"column": "vector", "q": vecs[i].values, "k": 5} for i in sample_query_indices
]
def has_target(target, results):
for item in results:
if item.values == target:
return True
return False
def check_index(has_knn_combined):
for query in sample_queries:
results = dataset.to_table(nearest=query).column("vector")
assert has_target(query["q"], results)
plan = dataset.scanner(nearest=query).explain_plan()
assert ("KNNVectorDistance" in plan) == has_knn_combined
# Original state is 2 indexed fragments of size 150. This should not require
# a combined scan
check_index(has_knn_combined=False)
# Compact the 2 fragments into 1. Combined scan still not needed.
dataset.optimize.compact_files()
assert len(dataset.get_fragments()) == 1
check_index(has_knn_combined=False)
# Add a new fragment and recalculate the index
extra_data = create_table(min=1000, max=1001, nvec=100)
dataset = lance.write_dataset(
extra_data, base_dir, mode="append", max_rows_per_file=100
)
dataset.create_index(
"vector", index_type="IVF_PQ", num_partitions=2, num_sub_vectors=2, replace=True
)
# Combined scan should not be needed
assert len(dataset.get_fragments()) == 2
check_index(has_knn_combined=False)
# Add a new unindexed fragment
extra_data = create_table(min=1000, max=1001, nvec=100)
dataset = lance.write_dataset(
extra_data, base_dir, mode="append", max_rows_per_file=100
)
assert len(dataset.get_fragments()) == 3
# Compaction should not combine the unindexed fragment with the indexed fragment
dataset.optimize.compact_files()
assert len(dataset.get_fragments()) == 2
# Now a combined scan is required
check_index(has_knn_combined=True)
def test_index_remapping_multiple_rewrite_tasks(tmp_path: Path):
base_dir = tmp_path / "dataset"
ds = lance.write_dataset(
create_table(min=0, max=1, nvec=300), base_dir, max_rows_per_file=150
)
ds = ds.create_index(
"vector",
index_type="IVF_PQ",
num_partitions=4,
num_sub_vectors=2,
)
assert ds.has_index
ds = lance.write_dataset(
create_table(min=0, max=1, nvec=300),
base_dir,
mode="append",
max_rows_per_file=150,
)
ds.delete("id % 4 == 0")
fragments = list(ds.get_fragments())
assert len(fragments) == 4
# We have a dataset with 4 small fragments. 2 are indexed and
# 2 are not. The indexed fragments and the non-indexed fragments
# cannot be combined and so we should end up with 2 fragments after
# compaction
ds.optimize.compact_files()
fragments = list(ds.get_fragments())
assert len(fragments) == 2
index = ds.list_indices()[0]
index_frag_ids = list(index["fragment_ids"])
frag_ids = [frag.fragment_id for frag in fragments]
assert len(index_frag_ids) == 1
assert index_frag_ids[0] in frag_ids
def test_dataset_distributed_optimize(tmp_path: Path):
base_dir = tmp_path / "dataset"
data = pa.table({"a": range(800), "b": range(800)})
dataset = lance.write_dataset(data, base_dir, max_rows_per_file=200)
fragments = dataset.get_fragments()
assert len(fragments) == 4
plan = Compaction.plan(
dataset, options=dict(target_rows_per_fragment=400, num_threads=1)
)
assert plan.read_version == 1
assert plan.num_tasks() == 2
assert plan.tasks[0].fragments == [frag.metadata for frag in fragments[0:2]]
assert plan.tasks[1].fragments == [frag.metadata for frag in fragments[2:4]]
assert repr(plan) == "CompactionPlan(read_version=1, tasks=<2 compaction tasks>)"
# Plan can be pickled
assert pickle.loads(pickle.dumps(plan)) == plan
pickled_task = pickle.dumps(plan.tasks[0])
task = pickle.loads(pickled_task)
assert task == plan.tasks[0]
result1 = plan.tasks[0].execute(dataset)
result1.metrics.fragments_removed == 2
result1.metrics.fragments_added == 1
pickled_result = pickle.dumps(result1)
result = pickle.loads(pickled_result)
assert isinstance(result, RewriteResult)
assert result == result1
assert re.match(
r"RewriteResult\(read_version=1, new_fragments=\[.+\], old_fragments=\[.+\]\)",
repr(result),
)
metrics = Compaction.commit(dataset, [result1])
assert metrics.fragments_removed == 2
assert metrics.fragments_added == 1
# Compaction occurs in two transactions so it increments the version by 2.
assert dataset.version == 3
def test_migration_via_fragment_apis(tmp_path):
"""
This test is a regression of a case where we were using fragment APIs to migrate
from v1 to v2 but that left the dataset in a state where it had v2 files but wasn't
marked with the v2 writer flag.
"""
data = pa.table({"a": range(800), "b": range(800)})
# Create v1 dataset
ds = lance.write_dataset(
data, tmp_path / "dataset", max_rows_per_file=200, data_storage_version="legacy"
)
# Create empty v2 dataset
lance.write_dataset(
data_obj=[],
uri=tmp_path / "dataset2",
schema=ds.schema,
data_storage_version="2.0",
)
# Add v2 files
fragments = []
for frag in ds.get_fragments():
reader = ds.scanner(fragments=[frag])
fragments.append(
lance.LanceFragment.create(
dataset_uri=tmp_path / "dataset2",
data=reader,
fragment_id=frag.fragment_id,
data_storage_version="2.0",
)
)
# Commit
operation = lance.LanceOperation.Overwrite(ds.schema, fragments)
ds2 = lance.LanceDataset.commit(tmp_path / "dataset2", operation)
# Compact, dataset should still be v2
ds2.optimize.compact_files()
ds2 = lance.dataset(tmp_path / "dataset2")
assert ds2.data_storage_version == "2.0"
def test_compaction_generates_rewrite_transaction(tmp_path: Path):
# Create a small dataset with multiple fragments
base_dir = tmp_path / "rewrite_txn"
data = pa.table({"a": range(300), "b": range(300)})
dataset = lance.write_dataset(data, base_dir, max_rows_per_file=100)
# Run compaction: should perform a rewrite (no deletions materialized)
dataset.optimize.compact_files(materialize_deletions=False, num_threads=1)
# Verify at least one transaction is a Rewrite; guard against None entries
transactions = dataset.get_transactions()
assert any(
t is not None and t.operation.__class__.__name__ == "Rewrite"
for t in transactions
)