peacock-data-public-datasets-idc-cronscript
/
venv
/lib
/python3.10
/site-packages
/pyarrow
/tests
/parquet
/test_dataset.py
# Licensed to the Apache Software Foundation (ASF) under one | |
# or more contributor license agreements. See the NOTICE file | |
# distributed with this work for additional information | |
# regarding copyright ownership. The ASF licenses this file | |
# to you under the Apache License, Version 2.0 (the | |
# "License"); you may not use this file except in compliance | |
# with the License. You may obtain a copy of the License at | |
# | |
# http://www.apache.org/licenses/LICENSE-2.0 | |
# | |
# Unless required by applicable law or agreed to in writing, | |
# software distributed under the License is distributed on an | |
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY | |
# KIND, either express or implied. See the License for the | |
# specific language governing permissions and limitations | |
# under the License. | |
import datetime | |
import inspect | |
import os | |
import pathlib | |
import numpy as np | |
import pytest | |
import unittest.mock as mock | |
import pyarrow as pa | |
import pyarrow.compute as pc | |
from pyarrow.fs import (FileSelector, FileSystem, LocalFileSystem, | |
PyFileSystem, SubTreeFileSystem, FSSpecHandler) | |
from pyarrow.tests import util | |
from pyarrow.util import guid | |
try: | |
import pyarrow.parquet as pq | |
from pyarrow.tests.parquet.common import ( | |
_read_table, _test_dataframe, _write_table) | |
except ImportError: | |
pq = None | |
try: | |
import pandas as pd | |
import pandas.testing as tm | |
except ImportError: | |
pd = tm = None | |
# Marks all of the tests in this module | |
# Ignore these with pytest ... -m 'not parquet' | |
pytestmark = [pytest.mark.parquet, pytest.mark.dataset] | |
def test_filesystem_uri(tempdir): | |
table = pa.table({"a": [1, 2, 3]}) | |
directory = tempdir / "data_dir" | |
directory.mkdir() | |
path = directory / "data.parquet" | |
pq.write_table(table, str(path)) | |
# filesystem object | |
result = pq.read_table( | |
path, filesystem=LocalFileSystem()) | |
assert result.equals(table) | |
# filesystem URI | |
result = pq.read_table( | |
"data_dir/data.parquet", filesystem=util._filesystem_uri(tempdir)) | |
assert result.equals(table) | |
def test_read_partitioned_directory(tempdir): | |
local = LocalFileSystem() | |
_partition_test_for_filesystem(local, tempdir) | |
def test_read_partitioned_columns_selection(tempdir): | |
# ARROW-3861 - do not include partition columns in resulting table when | |
# `columns` keyword was passed without those columns | |
local = LocalFileSystem() | |
base_path = tempdir | |
_partition_test_for_filesystem(local, base_path) | |
dataset = pq.ParquetDataset(base_path) | |
result = dataset.read(columns=["values"]) | |
assert result.column_names == ["values"] | |
def test_filters_equivalency(tempdir): | |
local = LocalFileSystem() | |
base_path = tempdir | |
integer_keys = [0, 1] | |
string_keys = ['a', 'b', 'c'] | |
boolean_keys = [True, False] | |
partition_spec = [ | |
['integer', integer_keys], | |
['string', string_keys], | |
['boolean', boolean_keys] | |
] | |
df = pd.DataFrame({ | |
'integer': np.array(integer_keys, dtype='i4').repeat(15), | |
'string': np.tile(np.tile(np.array(string_keys, dtype=object), 5), 2), | |
'boolean': np.tile(np.tile(np.array(boolean_keys, dtype='bool'), 5), 3), | |
'values': np.arange(30), | |
}) | |
_generate_partition_directories(local, base_path, partition_spec, df) | |
# Old filters syntax: | |
# integer == 1 AND string != b AND boolean == True | |
dataset = pq.ParquetDataset( | |
base_path, filesystem=local, | |
filters=[('integer', '=', 1), ('string', '!=', 'b'), | |
('boolean', '==', 'True')], | |
) | |
table = dataset.read() | |
result_df = (table.to_pandas().reset_index(drop=True)) | |
assert 0 not in result_df['integer'].values | |
assert 'b' not in result_df['string'].values | |
assert False not in result_df['boolean'].values | |
# filters in disjunctive normal form: | |
# (integer == 1 AND string != b AND boolean == True) OR | |
# (integer == 2 AND boolean == False) | |
# TODO(ARROW-3388): boolean columns are reconstructed as string | |
filters = [ | |
[ | |
('integer', '=', 1), | |
('string', '!=', 'b'), | |
('boolean', '==', 'True') | |
], | |
[('integer', '=', 0), ('boolean', '==', 'False')] | |
] | |
dataset = pq.ParquetDataset( | |
base_path, filesystem=local, filters=filters) | |
table = dataset.read() | |
result_df = table.to_pandas().reset_index(drop=True) | |
# Check that all rows in the DF fulfill the filter | |
df_filter_1 = (result_df['integer'] == 1) \ | |
& (result_df['string'] != 'b') \ | |
& (result_df['boolean'] == 'True') | |
df_filter_2 = (np.array(result_df['integer']) == 0) \ | |
& (result_df['boolean'] == 'False') | |
assert df_filter_1.sum() > 0 | |
assert df_filter_2.sum() > 0 | |
assert result_df.shape[0] == (df_filter_1.sum() + df_filter_2.sum()) | |
for filters in [[[('string', '==', b'1\0a')]], | |
[[('string', '==', '1\0a')]]]: | |
dataset = pq.ParquetDataset( | |
base_path, filesystem=local, filters=filters) | |
assert dataset.read().num_rows == 0 | |
def test_filters_cutoff_exclusive_integer(tempdir): | |
local = LocalFileSystem() | |
base_path = tempdir | |
integer_keys = [0, 1, 2, 3, 4] | |
partition_spec = [ | |
['integers', integer_keys], | |
] | |
N = 5 | |
df = pd.DataFrame({ | |
'index': np.arange(N), | |
'integers': np.array(integer_keys, dtype='i4'), | |
}, columns=['index', 'integers']) | |
_generate_partition_directories(local, base_path, partition_spec, df) | |
dataset = pq.ParquetDataset( | |
base_path, filesystem=local, | |
filters=[ | |
('integers', '<', 4), | |
('integers', '>', 1), | |
], | |
) | |
table = dataset.read() | |
result_df = (table.to_pandas() | |
.sort_values(by='index') | |
.reset_index(drop=True)) | |
result_list = [x for x in map(int, result_df['integers'].values)] | |
assert result_list == [2, 3] | |
def test_filters_cutoff_exclusive_datetime(tempdir): | |
local = LocalFileSystem() | |
base_path = tempdir | |
date_keys = [ | |
datetime.date(2018, 4, 9), | |
datetime.date(2018, 4, 10), | |
datetime.date(2018, 4, 11), | |
datetime.date(2018, 4, 12), | |
datetime.date(2018, 4, 13) | |
] | |
partition_spec = [ | |
['dates', date_keys] | |
] | |
N = 5 | |
df = pd.DataFrame({ | |
'index': np.arange(N), | |
'dates': np.array(date_keys, dtype='datetime64'), | |
}, columns=['index', 'dates']) | |
_generate_partition_directories(local, base_path, partition_spec, df) | |
dataset = pq.ParquetDataset( | |
base_path, filesystem=local, | |
filters=[ | |
('dates', '<', "2018-04-12"), | |
('dates', '>', "2018-04-10") | |
], | |
) | |
table = dataset.read() | |
result_df = (table.to_pandas() | |
.sort_values(by='index') | |
.reset_index(drop=True)) | |
expected = pd.Categorical( | |
np.array([datetime.date(2018, 4, 11)], dtype='datetime64'), | |
categories=np.array(date_keys, dtype='datetime64')) | |
assert result_df['dates'].values == expected | |
def test_filters_inclusive_datetime(tempdir): | |
# ARROW-11480 | |
path = tempdir / 'timestamps.parquet' | |
pd.DataFrame({ | |
"dates": pd.date_range("2020-01-01", periods=10, freq="D"), | |
"id": range(10) | |
}).to_parquet(path, use_deprecated_int96_timestamps=True) | |
table = pq.read_table(path, filters=[ | |
("dates", "<=", datetime.datetime(2020, 1, 5)) | |
]) | |
assert table.column('id').to_pylist() == [0, 1, 2, 3, 4] | |
def test_filters_inclusive_integer(tempdir): | |
local = LocalFileSystem() | |
base_path = tempdir | |
integer_keys = [0, 1, 2, 3, 4] | |
partition_spec = [ | |
['integers', integer_keys], | |
] | |
N = 5 | |
df = pd.DataFrame({ | |
'index': np.arange(N), | |
'integers': np.array(integer_keys, dtype='i4'), | |
}, columns=['index', 'integers']) | |
_generate_partition_directories(local, base_path, partition_spec, df) | |
dataset = pq.ParquetDataset( | |
base_path, filesystem=local, | |
filters=[ | |
('integers', '<=', 3), | |
('integers', '>=', 2), | |
], | |
) | |
table = dataset.read() | |
result_df = (table.to_pandas() | |
.sort_values(by='index') | |
.reset_index(drop=True)) | |
result_list = [int(x) for x in map(int, result_df['integers'].values)] | |
assert result_list == [2, 3] | |
def test_filters_inclusive_set(tempdir): | |
local = LocalFileSystem() | |
base_path = tempdir | |
integer_keys = [0, 1] | |
string_keys = ['a', 'b', 'c'] | |
boolean_keys = [True, False] | |
partition_spec = [ | |
['integer', integer_keys], | |
['string', string_keys], | |
['boolean', boolean_keys] | |
] | |
df = pd.DataFrame({ | |
'integer': np.array(integer_keys, dtype='i4').repeat(15), | |
'string': np.tile(np.tile(np.array(string_keys, dtype=object), 5), 2), | |
'boolean': np.tile(np.tile(np.array(boolean_keys, dtype='bool'), 5), 3), | |
'values': np.arange(30), | |
}) | |
_generate_partition_directories(local, base_path, partition_spec, df) | |
dataset = pq.ParquetDataset( | |
base_path, filesystem=local, | |
filters=[('string', 'in', 'ab')], | |
) | |
table = dataset.read() | |
result_df = (table.to_pandas().reset_index(drop=True)) | |
assert 'a' in result_df['string'].values | |
assert 'b' in result_df['string'].values | |
assert 'c' not in result_df['string'].values | |
dataset = pq.ParquetDataset( | |
base_path, filesystem=local, | |
filters=[('integer', 'in', [1]), ('string', 'in', ('a', 'b')), | |
('boolean', 'not in', {'False'})], | |
) | |
table = dataset.read() | |
result_df = (table.to_pandas().reset_index(drop=True)) | |
assert 0 not in result_df['integer'].values | |
assert 'c' not in result_df['string'].values | |
assert False not in result_df['boolean'].values | |
def test_filters_invalid_pred_op(tempdir): | |
local = LocalFileSystem() | |
base_path = tempdir | |
integer_keys = [0, 1, 2, 3, 4] | |
partition_spec = [ | |
['integers', integer_keys], | |
] | |
N = 5 | |
df = pd.DataFrame({ | |
'index': np.arange(N), | |
'integers': np.array(integer_keys, dtype='i4'), | |
}, columns=['index', 'integers']) | |
_generate_partition_directories(local, base_path, partition_spec, df) | |
with pytest.raises(TypeError): | |
pq.ParquetDataset(base_path, | |
filesystem=local, | |
filters=[('integers', 'in', 3), ]) | |
with pytest.raises(ValueError): | |
pq.ParquetDataset(base_path, | |
filesystem=local, | |
filters=[('integers', '=<', 3), ]) | |
# Dataset API returns empty table | |
dataset = pq.ParquetDataset(base_path, | |
filesystem=local, | |
filters=[('integers', 'in', set()), ]) | |
assert dataset.read().num_rows == 0 | |
dataset = pq.ParquetDataset(base_path, | |
filesystem=local, | |
filters=[('integers', '!=', {3})]) | |
with pytest.raises(NotImplementedError): | |
assert dataset.read().num_rows == 0 | |
def test_filters_invalid_column(tempdir): | |
# ARROW-5572 - raise error on invalid name in filter specification | |
# works with new dataset | |
local = LocalFileSystem() | |
base_path = tempdir | |
integer_keys = [0, 1, 2, 3, 4] | |
partition_spec = [['integers', integer_keys]] | |
N = 5 | |
df = pd.DataFrame({ | |
'index': np.arange(N), | |
'integers': np.array(integer_keys, dtype='i4'), | |
}, columns=['index', 'integers']) | |
_generate_partition_directories(local, base_path, partition_spec, df) | |
msg = r"No match for FieldRef.Name\(non_existent_column\)" | |
with pytest.raises(ValueError, match=msg): | |
pq.ParquetDataset(base_path, filesystem=local, | |
filters=[('non_existent_column', '<', 3), ]).read() | |
def test_filters_read_table(tempdir, filters, read_method): | |
read = getattr(pq, read_method) | |
# test that filters keyword is passed through in read_table | |
local = LocalFileSystem() | |
base_path = tempdir | |
integer_keys = [0, 1, 2, 3, 4] | |
partition_spec = [ | |
['integers', integer_keys], | |
] | |
N = len(integer_keys) | |
df = pd.DataFrame({ | |
'index': np.arange(N), | |
'integers': np.array(integer_keys, dtype='i4'), | |
'nested': np.array([{'a': i, 'b': str(i)} for i in range(N)]) | |
}) | |
_generate_partition_directories(local, base_path, partition_spec, df) | |
kwargs = dict(filesystem=local, filters=filters) | |
table = read(base_path, **kwargs) | |
assert table.num_rows == 3 | |
def test_partition_keys_with_underscores(tempdir): | |
# ARROW-5666 - partition field values with underscores preserve underscores | |
local = LocalFileSystem() | |
base_path = tempdir | |
string_keys = ["2019_2", "2019_3"] | |
partition_spec = [ | |
['year_week', string_keys], | |
] | |
N = 2 | |
df = pd.DataFrame({ | |
'index': np.arange(N), | |
'year_week': np.array(string_keys, dtype='object'), | |
}, columns=['index', 'year_week']) | |
_generate_partition_directories(local, base_path, partition_spec, df) | |
dataset = pq.ParquetDataset(base_path) | |
result = dataset.read() | |
assert result.column("year_week").to_pylist() == string_keys | |
def test_read_s3fs(s3_example_s3fs, ): | |
fs, path = s3_example_s3fs | |
path = path + "/test.parquet" | |
table = pa.table({"a": [1, 2, 3]}) | |
_write_table(table, path, filesystem=fs) | |
result = _read_table(path, filesystem=fs) | |
assert result.equals(table) | |
def test_read_directory_s3fs(s3_example_s3fs): | |
fs, directory = s3_example_s3fs | |
path = directory + "/test.parquet" | |
table = pa.table({"a": [1, 2, 3]}) | |
_write_table(table, path, filesystem=fs) | |
result = _read_table(directory, filesystem=fs) | |
assert result.equals(table) | |
def test_read_single_file_list(tempdir): | |
data_path = str(tempdir / 'data.parquet') | |
table = pa.table({"a": [1, 2, 3]}) | |
_write_table(table, data_path) | |
result = pq.ParquetDataset([data_path]).read() | |
assert result.equals(table) | |
def test_read_partitioned_directory_s3fs(s3_example_s3fs): | |
fs, path = s3_example_s3fs | |
_partition_test_for_filesystem(fs, path) | |
def _partition_test_for_filesystem(fs, base_path): | |
foo_keys = [0, 1] | |
bar_keys = ['a', 'b', 'c'] | |
partition_spec = [ | |
['foo', foo_keys], | |
['bar', bar_keys] | |
] | |
N = 30 | |
df = pd.DataFrame({ | |
'index': np.arange(N), | |
'foo': np.array(foo_keys, dtype='i4').repeat(15), | |
'bar': np.tile(np.tile(np.array(bar_keys, dtype=object), 5), 2), | |
'values': np.random.randn(N) | |
}, columns=['index', 'foo', 'bar', 'values']) | |
_generate_partition_directories(fs, base_path, partition_spec, df) | |
dataset = pq.ParquetDataset(base_path, filesystem=fs) | |
table = dataset.read() | |
result_df = (table.to_pandas() | |
.sort_values(by='index') | |
.reset_index(drop=True)) | |
expected_df = (df.sort_values(by='index') | |
.reset_index(drop=True) | |
.reindex(columns=result_df.columns)) | |
# With pandas 2.0.0 Index can store all numeric dtypes (not just | |
# int64/uint64/float64). Using astype() to create a categorical | |
# column preserves original dtype (int32) | |
expected_df['foo'] = expected_df['foo'].astype("category") | |
expected_df['bar'] = expected_df['bar'].astype("category") | |
assert (result_df.columns == ['index', 'values', 'foo', 'bar']).all() | |
tm.assert_frame_equal(result_df, expected_df) | |
def _generate_partition_directories(fs, base_dir, partition_spec, df): | |
# partition_spec : list of lists, e.g. [['foo', [0, 1, 2], | |
# ['bar', ['a', 'b', 'c']] | |
# part_table : a pyarrow.Table to write to each partition | |
if not isinstance(fs, FileSystem): | |
fs = PyFileSystem(FSSpecHandler(fs)) | |
DEPTH = len(partition_spec) | |
pathsep = getattr(fs, "pathsep", getattr(fs, "sep", "/")) | |
def _visit_level(base_dir, level, part_keys): | |
name, values = partition_spec[level] | |
for value in values: | |
this_part_keys = part_keys + [(name, value)] | |
level_dir = pathsep.join([ | |
str(base_dir), | |
'{}={}'.format(name, value) | |
]) | |
fs.create_dir(level_dir) | |
if level == DEPTH - 1: | |
# Generate example data | |
from pyarrow.fs import FileType | |
file_path = pathsep.join([level_dir, guid()]) | |
filtered_df = _filter_partition(df, this_part_keys) | |
part_table = pa.Table.from_pandas(filtered_df) | |
with fs.open_output_stream(file_path) as f: | |
_write_table(part_table, f) | |
assert fs.get_file_info(file_path).type != FileType.NotFound | |
assert fs.get_file_info(file_path).type == FileType.File | |
file_success = pathsep.join([level_dir, '_SUCCESS']) | |
with fs.open_output_stream(file_success) as f: | |
pass | |
else: | |
_visit_level(level_dir, level + 1, this_part_keys) | |
file_success = pathsep.join([level_dir, '_SUCCESS']) | |
with fs.open_output_stream(file_success) as f: | |
pass | |
_visit_level(base_dir, 0, []) | |
def _filter_partition(df, part_keys): | |
predicate = np.ones(len(df), dtype=bool) | |
to_drop = [] | |
for name, value in part_keys: | |
to_drop.append(name) | |
# to avoid pandas warning | |
if isinstance(value, (datetime.date, datetime.datetime)): | |
value = pd.Timestamp(value) | |
predicate &= df[name] == value | |
return df[predicate].drop(to_drop, axis=1) | |
def test_filter_before_validate_schema(tempdir): | |
# ARROW-4076 apply filter before schema validation | |
# to avoid checking unneeded schemas | |
# create partitioned dataset with mismatching schemas which would | |
# otherwise raise if first validation all schemas | |
dir1 = tempdir / 'A=0' | |
dir1.mkdir() | |
table1 = pa.Table.from_pandas(pd.DataFrame({'B': [1, 2, 3]})) | |
pq.write_table(table1, dir1 / 'data.parquet') | |
dir2 = tempdir / 'A=1' | |
dir2.mkdir() | |
table2 = pa.Table.from_pandas(pd.DataFrame({'B': ['a', 'b', 'c']})) | |
pq.write_table(table2, dir2 / 'data.parquet') | |
# read single file using filter | |
table = pq.read_table(tempdir, filters=[[('A', '==', 0)]]) | |
assert table.column('B').equals(pa.chunked_array([[1, 2, 3]])) | |
def test_read_multiple_files(tempdir): | |
nfiles = 10 | |
size = 5 | |
dirpath = tempdir / guid() | |
dirpath.mkdir() | |
test_data = [] | |
paths = [] | |
for i in range(nfiles): | |
df = _test_dataframe(size, seed=i) | |
# Hack so that we don't have a dtype cast in v1 files | |
df['uint32'] = df['uint32'].astype(np.int64) | |
path = dirpath / '{}.parquet'.format(i) | |
table = pa.Table.from_pandas(df) | |
_write_table(table, path) | |
test_data.append(table) | |
paths.append(path) | |
# Write a _SUCCESS.crc file | |
(dirpath / '_SUCCESS.crc').touch() | |
def read_multiple_files(paths, columns=None, use_threads=True, **kwargs): | |
dataset = pq.ParquetDataset(paths, **kwargs) | |
return dataset.read(columns=columns, use_threads=use_threads) | |
result = read_multiple_files(paths) | |
expected = pa.concat_tables(test_data) | |
assert result.equals(expected) | |
# Read column subset | |
to_read = [0, 2, 6, result.num_columns - 1] | |
col_names = [result.field(i).name for i in to_read] | |
out = pq.read_table(dirpath, columns=col_names) | |
expected = pa.Table.from_arrays([result.column(i) for i in to_read], | |
names=col_names, | |
metadata=result.schema.metadata) | |
assert out.equals(expected) | |
# Read with multiple threads | |
pq.read_table(dirpath, use_threads=True) | |
# Test failure modes with non-uniform metadata | |
bad_apple = _test_dataframe(size, seed=i).iloc[:, :4] | |
bad_apple_path = tempdir / '{}.parquet'.format(guid()) | |
t = pa.Table.from_pandas(bad_apple) | |
_write_table(t, bad_apple_path) | |
# TODO(dataset) Dataset API skips bad files | |
# bad_meta = pq.read_metadata(bad_apple_path) | |
# with pytest.raises(ValueError): | |
# read_multiple_files(paths + [bad_apple_path]) | |
# with pytest.raises(ValueError): | |
# read_multiple_files(paths, metadata=bad_meta) | |
# mixed_paths = [bad_apple_path, paths[0]] | |
# with pytest.raises(ValueError): | |
# read_multiple_files(mixed_paths) | |
def test_dataset_read_pandas(tempdir): | |
nfiles = 5 | |
size = 5 | |
dirpath = tempdir / guid() | |
dirpath.mkdir() | |
test_data = [] | |
frames = [] | |
paths = [] | |
for i in range(nfiles): | |
df = _test_dataframe(size, seed=i) | |
df.index = np.arange(i * size, (i + 1) * size) | |
df.index.name = 'index' | |
path = dirpath / '{}.parquet'.format(i) | |
table = pa.Table.from_pandas(df) | |
_write_table(table, path) | |
test_data.append(table) | |
frames.append(df) | |
paths.append(path) | |
dataset = pq.ParquetDataset(dirpath) | |
columns = ['uint8', 'strings'] | |
result = dataset.read_pandas(columns=columns).to_pandas() | |
expected = pd.concat([x[columns] for x in frames]) | |
tm.assert_frame_equal(result, expected) | |
# also be able to pass the columns as a set (ARROW-12314) | |
result = dataset.read_pandas(columns=set(columns)).to_pandas() | |
assert result.shape == expected.shape | |
# column order can be different because of using a set | |
tm.assert_frame_equal(result.reindex(columns=expected.columns), expected) | |
def test_dataset_memory_map(tempdir): | |
# ARROW-2627: Check that we can use ParquetDataset with memory-mapping | |
dirpath = tempdir / guid() | |
dirpath.mkdir() | |
df = _test_dataframe(10, seed=0) | |
path = dirpath / '{}.parquet'.format(0) | |
table = pa.Table.from_pandas(df) | |
_write_table(table, path, version='2.6') | |
dataset = pq.ParquetDataset( | |
dirpath, memory_map=True) | |
assert dataset.read().equals(table) | |
def test_dataset_enable_buffered_stream(tempdir): | |
dirpath = tempdir / guid() | |
dirpath.mkdir() | |
df = _test_dataframe(10, seed=0) | |
path = dirpath / '{}.parquet'.format(0) | |
table = pa.Table.from_pandas(df) | |
_write_table(table, path, version='2.6') | |
with pytest.raises(ValueError): | |
pq.ParquetDataset( | |
dirpath, buffer_size=-64) | |
for buffer_size in [128, 1024]: | |
dataset = pq.ParquetDataset( | |
dirpath, buffer_size=buffer_size) | |
assert dataset.read().equals(table) | |
def test_dataset_enable_pre_buffer(tempdir): | |
dirpath = tempdir / guid() | |
dirpath.mkdir() | |
df = _test_dataframe(10, seed=0) | |
path = dirpath / '{}.parquet'.format(0) | |
table = pa.Table.from_pandas(df) | |
_write_table(table, path, version='2.6') | |
for pre_buffer in (True, False): | |
dataset = pq.ParquetDataset( | |
dirpath, pre_buffer=pre_buffer) | |
assert dataset.read().equals(table) | |
actual = pq.read_table(dirpath, pre_buffer=pre_buffer) | |
assert actual.equals(table) | |
def _make_example_multifile_dataset(base_path, nfiles=10, file_nrows=5): | |
test_data = [] | |
paths = [] | |
for i in range(nfiles): | |
df = _test_dataframe(file_nrows, seed=i) | |
path = base_path / '{}.parquet'.format(i) | |
test_data.append(_write_table(df, path)) | |
paths.append(path) | |
return paths | |
def _assert_dataset_paths(dataset, paths): | |
paths = [str(path.as_posix()) for path in paths] | |
assert set(paths) == set(dataset.files) | |
def test_ignore_private_directories(tempdir, dir_prefix): | |
dirpath = tempdir / guid() | |
dirpath.mkdir() | |
paths = _make_example_multifile_dataset(dirpath, nfiles=10, | |
file_nrows=5) | |
# private directory | |
(dirpath / '{}staging'.format(dir_prefix)).mkdir() | |
dataset = pq.ParquetDataset(dirpath) | |
_assert_dataset_paths(dataset, paths) | |
def test_ignore_hidden_files_dot(tempdir): | |
dirpath = tempdir / guid() | |
dirpath.mkdir() | |
paths = _make_example_multifile_dataset(dirpath, nfiles=10, | |
file_nrows=5) | |
with (dirpath / '.DS_Store').open('wb') as f: | |
f.write(b'gibberish') | |
with (dirpath / '.private').open('wb') as f: | |
f.write(b'gibberish') | |
dataset = pq.ParquetDataset(dirpath) | |
_assert_dataset_paths(dataset, paths) | |
def test_ignore_hidden_files_underscore(tempdir): | |
dirpath = tempdir / guid() | |
dirpath.mkdir() | |
paths = _make_example_multifile_dataset(dirpath, nfiles=10, | |
file_nrows=5) | |
with (dirpath / '_committed_123').open('wb') as f: | |
f.write(b'abcd') | |
with (dirpath / '_started_321').open('wb') as f: | |
f.write(b'abcd') | |
dataset = pq.ParquetDataset(dirpath) | |
_assert_dataset_paths(dataset, paths) | |
def test_ignore_no_private_directories_in_base_path(tempdir, dir_prefix): | |
# ARROW-8427 - don't ignore explicitly listed files if parent directory | |
# is a private directory | |
dirpath = tempdir / "{0}data".format(dir_prefix) / guid() | |
dirpath.mkdir(parents=True) | |
paths = _make_example_multifile_dataset(dirpath, nfiles=10, | |
file_nrows=5) | |
dataset = pq.ParquetDataset(paths) | |
_assert_dataset_paths(dataset, paths) | |
# ARROW-9644 - don't ignore full directory with underscore in base path | |
dataset = pq.ParquetDataset(dirpath) | |
_assert_dataset_paths(dataset, paths) | |
def test_ignore_custom_prefixes(tempdir): | |
# ARROW-9573 - allow override of default ignore_prefixes | |
part = ["xxx"] * 3 + ["yyy"] * 3 | |
table = pa.table([ | |
pa.array(range(len(part))), | |
pa.array(part).dictionary_encode(), | |
], names=['index', '_part']) | |
pq.write_to_dataset(table, str(tempdir), partition_cols=['_part']) | |
private_duplicate = tempdir / '_private_duplicate' | |
private_duplicate.mkdir() | |
pq.write_to_dataset(table, str(private_duplicate), | |
partition_cols=['_part']) | |
read = pq.read_table( | |
tempdir, ignore_prefixes=['_private']) | |
assert read.equals(table) | |
def test_empty_directory(tempdir): | |
# ARROW-5310 | |
empty_dir = tempdir / 'dataset' | |
empty_dir.mkdir() | |
dataset = pq.ParquetDataset(empty_dir) | |
result = dataset.read() | |
assert result.num_rows == 0 | |
assert result.num_columns == 0 | |
def _test_write_to_dataset_with_partitions(base_path, | |
filesystem=None, | |
schema=None, | |
index_name=None): | |
import pandas as pd | |
import pandas.testing as tm | |
import pyarrow.parquet as pq | |
# ARROW-1400 | |
output_df = pd.DataFrame({ | |
'group1': list('aaabbbbccc'), | |
'group2': list('eefeffgeee'), | |
'num': list(range(10)), | |
'nan': [np.nan] * 10, | |
'date': np.arange('2017-01-01', '2017-01-11', dtype='datetime64[D]').astype( | |
'datetime64[ns]') | |
}) | |
cols = output_df.columns.tolist() | |
partition_by = ['group1', 'group2'] | |
output_table = pa.Table.from_pandas(output_df, schema=schema, safe=False, | |
preserve_index=False) | |
pq.write_to_dataset(output_table, base_path, partition_by, | |
filesystem=filesystem) | |
metadata_path = os.path.join(str(base_path), '_common_metadata') | |
if filesystem is not None: | |
with filesystem.open(metadata_path, 'wb') as f: | |
pq.write_metadata(output_table.schema, f) | |
else: | |
pq.write_metadata(output_table.schema, metadata_path) | |
dataset = pq.ParquetDataset(base_path, | |
filesystem=filesystem) | |
# ARROW-2209: Ensure the dataset schema also includes the partition columns | |
# NB schema property is an arrow and not parquet schema | |
dataset_cols = set(dataset.schema.names) | |
assert dataset_cols == set(output_table.schema.names) | |
input_table = dataset.read() | |
input_df = input_table.to_pandas() | |
# Read data back in and compare with original DataFrame | |
# Partitioned columns added to the end of the DataFrame when read | |
input_df_cols = input_df.columns.tolist() | |
assert partition_by == input_df_cols[-1 * len(partition_by):] | |
input_df = input_df[cols] | |
# Partitioned columns become 'categorical' dtypes | |
for col in partition_by: | |
output_df[col] = output_df[col].astype('category') | |
if schema: | |
expected_date_type = schema.field('date').type.to_pandas_dtype() | |
output_df["date"] = output_df["date"].astype(expected_date_type) | |
tm.assert_frame_equal(output_df, input_df) | |
def _test_write_to_dataset_no_partitions(base_path, | |
filesystem=None): | |
import pandas as pd | |
import pyarrow.parquet as pq | |
# ARROW-1400 | |
output_df = pd.DataFrame({ | |
'group1': list('aaabbbbccc'), | |
'group2': list('eefeffgeee'), | |
'num': list(range(10)), | |
'date': np.arange('2017-01-01', '2017-01-11', dtype='datetime64[D]').astype( | |
'datetime64[ns]') | |
}) | |
cols = output_df.columns.tolist() | |
output_table = pa.Table.from_pandas(output_df) | |
if filesystem is None: | |
filesystem = LocalFileSystem() | |
elif not isinstance(filesystem, FileSystem): | |
filesystem = PyFileSystem(FSSpecHandler(filesystem)) | |
# Without partitions, append files to root_path | |
n = 5 | |
for i in range(n): | |
pq.write_to_dataset(output_table, base_path, | |
filesystem=filesystem) | |
selector = FileSelector(str(base_path), allow_not_found=False, | |
recursive=True) | |
infos = filesystem.get_file_info(selector) | |
output_files = [info for info in infos if info.path.endswith(".parquet")] | |
assert len(output_files) == n | |
# Deduplicated incoming DataFrame should match | |
# original outgoing Dataframe | |
input_table = pq.ParquetDataset( | |
base_path, filesystem=filesystem | |
).read() | |
input_df = input_table.to_pandas() | |
input_df = input_df.drop_duplicates() | |
input_df = input_df[cols] | |
tm.assert_frame_equal(output_df, input_df) | |
def test_write_to_dataset_with_partitions(tempdir): | |
_test_write_to_dataset_with_partitions(str(tempdir)) | |
def test_write_to_dataset_with_partitions_and_schema(tempdir): | |
schema = pa.schema([pa.field('group1', type=pa.string()), | |
pa.field('group2', type=pa.string()), | |
pa.field('num', type=pa.int64()), | |
pa.field('nan', type=pa.int32()), | |
pa.field('date', type=pa.timestamp(unit='us'))]) | |
_test_write_to_dataset_with_partitions( | |
str(tempdir), schema=schema) | |
def test_write_to_dataset_with_partitions_and_index_name(tempdir): | |
_test_write_to_dataset_with_partitions( | |
str(tempdir), index_name='index_name') | |
def test_write_to_dataset_no_partitions(tempdir): | |
_test_write_to_dataset_no_partitions(str(tempdir)) | |
def test_write_to_dataset_pathlib(tempdir): | |
_test_write_to_dataset_with_partitions(tempdir / "test1") | |
_test_write_to_dataset_no_partitions(tempdir / "test2") | |
def test_write_to_dataset_pathlib_nonlocal(tempdir, s3_example_s3fs): | |
# pathlib paths are only accepted for local files | |
fs, _ = s3_example_s3fs | |
with pytest.raises(TypeError, match="path-like objects are only allowed"): | |
_test_write_to_dataset_with_partitions( | |
tempdir / "test1", filesystem=fs) | |
with pytest.raises(TypeError, match="path-like objects are only allowed"): | |
_test_write_to_dataset_no_partitions( | |
tempdir / "test2", filesystem=fs) | |
def test_write_to_dataset_with_partitions_s3fs(s3_example_s3fs): | |
fs, path = s3_example_s3fs | |
_test_write_to_dataset_with_partitions( | |
path, filesystem=fs) | |
def test_write_to_dataset_no_partitions_s3fs(s3_example_s3fs): | |
fs, path = s3_example_s3fs | |
_test_write_to_dataset_no_partitions( | |
path, filesystem=fs) | |
def test_write_to_dataset_filesystem(tempdir): | |
df = pd.DataFrame({'A': [1, 2, 3]}) | |
table = pa.Table.from_pandas(df) | |
path = str(tempdir) | |
pq.write_to_dataset(table, path, filesystem=LocalFileSystem()) | |
result = pq.read_table(path) | |
assert result.equals(table) | |
def _make_dataset_for_pickling(tempdir, N=100): | |
path = tempdir / 'data.parquet' | |
local = LocalFileSystem() | |
df = pd.DataFrame({ | |
'index': np.arange(N), | |
'values': np.random.randn(N) | |
}, columns=['index', 'values']) | |
table = pa.Table.from_pandas(df) | |
num_groups = 3 | |
with pq.ParquetWriter(path, table.schema) as writer: | |
for i in range(num_groups): | |
writer.write_table(table) | |
reader = pq.ParquetFile(path) | |
assert reader.metadata.num_row_groups == num_groups | |
metadata_path = tempdir / '_metadata' | |
with local.open_output_stream(str(metadata_path)) as f: | |
pq.write_metadata(table.schema, f) | |
dataset = pq.ParquetDataset( | |
tempdir, filesystem=local) | |
return dataset | |
def test_pickle_dataset(tempdir, pickle_module): | |
def is_pickleable(obj): | |
return obj == pickle_module.loads(pickle_module.dumps(obj)) | |
dataset = _make_dataset_for_pickling(tempdir) | |
assert is_pickleable(dataset) | |
def test_partitioned_dataset(tempdir): | |
# ARROW-3208: Segmentation fault when reading a Parquet partitioned dataset | |
# to a Parquet file | |
path = tempdir / "ARROW-3208" | |
df = pd.DataFrame({ | |
'one': [-1, 10, 2.5, 100, 1000, 1, 29.2], | |
'two': [-1, 10, 2, 100, 1000, 1, 11], | |
'three': [0, 0, 0, 0, 0, 0, 0] | |
}) | |
table = pa.Table.from_pandas(df) | |
pq.write_to_dataset(table, root_path=str(path), | |
partition_cols=['one', 'two']) | |
table = pq.ParquetDataset(path).read() | |
pq.write_table(table, path / "output.parquet") | |
def test_dataset_read_dictionary(tempdir): | |
path = tempdir / "ARROW-3325-dataset" | |
t1 = pa.table([[util.rands(10) for i in range(5)] * 10], names=['f0']) | |
t2 = pa.table([[util.rands(10) for i in range(5)] * 10], names=['f0']) | |
pq.write_to_dataset(t1, root_path=str(path)) | |
pq.write_to_dataset(t2, root_path=str(path)) | |
result = pq.ParquetDataset( | |
path, read_dictionary=['f0']).read() | |
# The order of the chunks is non-deterministic | |
ex_chunks = [t1[0].chunk(0).dictionary_encode(), | |
t2[0].chunk(0).dictionary_encode()] | |
assert result[0].num_chunks == 2 | |
c0, c1 = result[0].chunk(0), result[0].chunk(1) | |
if c0.equals(ex_chunks[0]): | |
assert c1.equals(ex_chunks[1]) | |
else: | |
assert c0.equals(ex_chunks[1]) | |
assert c1.equals(ex_chunks[0]) | |
def test_read_table_schema(tempdir): | |
# test that schema keyword is passed through in read_table | |
table = pa.table({'a': pa.array([1, 2, 3], pa.int32())}) | |
pq.write_table(table, tempdir / "data1.parquet") | |
pq.write_table(table, tempdir / "data2.parquet") | |
schema = pa.schema([('a', 'int64')]) | |
# reading single file (which is special cased in the code) | |
result = pq.read_table(tempdir / "data1.parquet", schema=schema) | |
expected = pa.table({'a': [1, 2, 3]}, schema=schema) | |
assert result.equals(expected) | |
# reading multiple fields | |
result = pq.read_table(tempdir, schema=schema) | |
expected = pa.table({'a': [1, 2, 3, 1, 2, 3]}, schema=schema) | |
assert result.equals(expected) | |
result = pq.ParquetDataset(tempdir, schema=schema) | |
expected = pa.table({'a': [1, 2, 3, 1, 2, 3]}, schema=schema) | |
assert result.read().equals(expected) | |
def test_read_table_duplicate_column_selection(tempdir): | |
# test that duplicate column selection gives duplicate columns | |
table = pa.table({'a': pa.array([1, 2, 3], pa.int32()), | |
'b': pa.array([1, 2, 3], pa.uint8())}) | |
pq.write_table(table, tempdir / "data.parquet") | |
result = pq.read_table(tempdir / "data.parquet", columns=['a', 'a']) | |
expected_schema = pa.schema([('a', 'int32'), ('a', 'int32')]) | |
assert result.column_names == ['a', 'a'] | |
assert result.schema == expected_schema | |
def test_dataset_partitioning(tempdir): | |
import pyarrow.dataset as ds | |
# create small dataset with directory partitioning | |
root_path = tempdir / "test_partitioning" | |
(root_path / "2012" / "10" / "01").mkdir(parents=True) | |
table = pa.table({'a': [1, 2, 3]}) | |
pq.write_table( | |
table, str(root_path / "2012" / "10" / "01" / "data.parquet")) | |
# This works with new dataset API | |
# read_table | |
part = ds.partitioning(field_names=["year", "month", "day"]) | |
result = pq.read_table( | |
str(root_path), partitioning=part) | |
assert result.column_names == ["a", "year", "month", "day"] | |
result = pq.ParquetDataset( | |
str(root_path), partitioning=part).read() | |
assert result.column_names == ["a", "year", "month", "day"] | |
def test_parquet_dataset_new_filesystem(tempdir): | |
# Ensure we can pass new FileSystem object to ParquetDataset | |
table = pa.table({'a': [1, 2, 3]}) | |
pq.write_table(table, tempdir / 'data.parquet') | |
filesystem = SubTreeFileSystem(str(tempdir), LocalFileSystem()) | |
dataset = pq.ParquetDataset('.', filesystem=filesystem) | |
result = dataset.read() | |
assert result.equals(table) | |
def test_parquet_dataset_partitions_piece_path_with_fsspec(tempdir): | |
# ARROW-10462 ensure that on Windows we properly use posix-style paths | |
# as used by fsspec | |
fsspec = pytest.importorskip("fsspec") | |
filesystem = fsspec.filesystem('file') | |
table = pa.table({'a': [1, 2, 3]}) | |
pq.write_table(table, tempdir / 'data.parquet') | |
# pass a posix-style path (using "/" also on Windows) | |
path = str(tempdir).replace("\\", "/") | |
dataset = pq.ParquetDataset( | |
path, filesystem=filesystem) | |
# ensure the piece path is also posix-style | |
expected = path + "/data.parquet" | |
assert dataset.fragments[0].path == expected | |
def test_parquet_write_to_dataset_exposed_keywords(tempdir): | |
table = pa.table({'a': [1, 2, 3]}) | |
path = tempdir / 'partitioning' | |
paths_written = [] | |
def file_visitor(written_file): | |
paths_written.append(written_file.path) | |
basename_template = 'part-{i}.parquet' | |
pq.write_to_dataset(table, path, partitioning=["a"], | |
file_visitor=file_visitor, | |
basename_template=basename_template) | |
expected_paths = { | |
path / '1' / 'part-0.parquet', | |
path / '2' / 'part-0.parquet', | |
path / '3' / 'part-0.parquet' | |
} | |
paths_written_set = set(map(pathlib.Path, paths_written)) | |
assert paths_written_set == expected_paths | |
def test_write_to_dataset_kwargs_passed(tempdir, write_dataset_kwarg): | |
"""Verify kwargs in pq.write_to_dataset are passed onto ds.write_dataset""" | |
import pyarrow.dataset as ds | |
table = pa.table({"a": [1, 2, 3]}) | |
path = tempdir / 'out.parquet' | |
signature = inspect.signature(ds.write_dataset) | |
key, arg = write_dataset_kwarg | |
# kwarg not in pq.write_to_dataset, but will be passed to ds.write_dataset | |
assert key not in inspect.signature(pq.write_to_dataset).parameters | |
assert key in signature.parameters | |
with mock.patch.object(ds, "write_dataset", autospec=True)\ | |
as mock_write_dataset: | |
pq.write_to_dataset(table, path, **{key: arg}) | |
_name, _args, kwargs = mock_write_dataset.mock_calls[0] | |
assert kwargs[key] == arg | |
def test_write_to_dataset_category_observed(tempdir): | |
# if we partition on a categorical variable with "unobserved" categories | |
# (values present in the dictionary, but not in the actual data) | |
# ensure those are not creating empty files/directories | |
df = pd.DataFrame({ | |
"cat": pd.Categorical(["a", "b", "a"], categories=["a", "b", "c"]), | |
"col": [1, 2, 3] | |
}) | |
table = pa.table(df) | |
path = tempdir / "dataset" | |
pq.write_to_dataset( | |
table, tempdir / "dataset", partition_cols=["cat"] | |
) | |
subdirs = [f.name for f in path.iterdir() if f.is_dir()] | |
assert len(subdirs) == 2 | |
assert "cat=c" not in subdirs | |