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import os
import pathlib
import random
import sys
import numpy as np
import pytest
import tiledb
from .common import DiskTestCase, rand_utf8
class TestVFS(DiskTestCase):
def test_supports(self):
vfs = tiledb.VFS()
self.assertTrue(vfs.supports("file"))
self.assertIsInstance(vfs.supports("s3"), bool)
self.assertIsInstance(vfs.supports("hdfs"), bool)
self.assertIsInstance(vfs.supports("gcs"), bool)
self.assertIsInstance(vfs.supports("azure"), bool)
with self.assertRaises(ValueError):
vfs.supports("invalid")
def test_vfs_config(self):
opt = {"region": "us-west-x1234"}
params = [opt, tiledb.Config(opt)]
for param in params:
vfs = tiledb.VFS(param)
assert vfs.config()["region"] == opt["region"]
def test_dir(self):
vfs = tiledb.VFS()
dir = self.path("foo")
self.assertFalse(vfs.is_dir(dir))
# create
vfs.create_dir(dir)
if pytest.tiledb_vfs != "s3":
self.assertTrue(vfs.is_dir(dir))
# remove
vfs.remove_dir(dir)
self.assertFalse(vfs.is_dir(dir))
# create nested path
dir = self.path("foo/bar")
if pytest.tiledb_vfs != "s3":
# this fails locally because "foo" base path does not exist
# this will not fail on s3 because there is no concept of directory
with self.assertRaises(tiledb.TileDBError):
vfs.create_dir(dir)
vfs.create_dir(self.path("foo"))
vfs.create_dir(self.path("foo/bar"))
if pytest.tiledb_vfs != "s3":
self.assertTrue(vfs.is_dir(dir))
def test_file(self):
vfs = tiledb.VFS()
file = self.path("foo")
self.assertFalse(vfs.is_file(file))
# create
vfs.touch(file)
self.assertTrue(vfs.is_file(file))
# remove
vfs.remove_file(file)
self.assertFalse(vfs.is_file(file))
# check nested path
file = self.path("foo/bar")
if pytest.tiledb_vfs != "s3":
# this fails locally because "foo" base path does not exist
# this will not fail on s3 because there is no concept of directory
with self.assertRaises(tiledb.TileDBError):
vfs.touch(file)
def test_move(self):
vfs = tiledb.VFS()
vfs.create_dir(self.path("foo"))
vfs.create_dir(self.path("bar"))
vfs.touch(self.path("bar/baz"))
self.assertTrue(vfs.is_file(self.path("bar/baz")))
vfs.move_file(self.path("bar/baz"), self.path("foo/baz"))
self.assertFalse(vfs.is_file(self.path("bar/baz")))
self.assertTrue(vfs.is_file(self.path("foo/baz")))
# moving to invalid dir should raise an error
if pytest.tiledb_vfs != "s3":
# this fails locally because "foo" base path does not exist
# this will not fail on s3 because there is no concept of directory
with self.assertRaises(tiledb.TileDBError):
vfs.move_dir(self.path("foo/baz"), self.path("do_not_exist/baz"))
@pytest.mark.skipif(
sys.platform == "win32",
reason="VFS copy commands from core are not supported on Windows",
)
def test_copy(self):
vfs = tiledb.VFS()
vfs.create_dir(self.path("foo"))
vfs.create_dir(self.path("bar"))
vfs.touch(self.path("foo/baz"))
self.assertTrue(vfs.is_file(self.path("foo/baz")))
vfs.copy_file(self.path("foo/baz"), self.path("bar/baz"))
self.assertTrue(vfs.is_file(self.path("foo/baz")))
self.assertTrue(vfs.is_file(self.path("bar/baz")))
vfs.copy_dir(self.path("foo"), self.path("baz"))
self.assertTrue(vfs.is_file(self.path("baz/baz")))
# copying to invalid dir should raise an error
if pytest.tiledb_vfs != "s3":
# this fails locally because "foo" base path does not exist
# this will not fail on s3 because there is no concept of directory
with self.assertRaises(tiledb.TileDBError):
vfs.copy_dir(self.path("foo/baz"), self.path("do_not_exist/baz"))
def test_write_read(self):
vfs = tiledb.VFS()
buffer = b"bar"
fio = vfs.open(pathlib.Path(self.path("foo")), "wb")
fio.write(buffer)
self.assertEqual(vfs.file_size(self.path("foo")), 3)
fio = vfs.open(self.path("foo").encode("utf-8"), "rb")
self.assertEqual(fio.read(3), buffer)
# test read with numpy integers
fio.seek(np.int64(0))
self.assertEqual(fio.read(np.int32(3)), buffer)
fio.seek(np.int64(0))
self.assertEqual(fio.read(np.uint64(3)), buffer)
fio.close()
# write / read empty input
fio = vfs.open(self.path("baz"), "wb")
fio.write(b"")
fio.close()
self.assertEqual(vfs.file_size(self.path("baz")), 0)
fio = vfs.open(self.path("baz"), "rb")
self.assertEqual(fio.read(0), b"")
fio.close()
# read from file that does not exist
with self.assertRaises(tiledb.TileDBError):
vfs.open(self.path("do_not_exist"), "rb")
def test_io(self):
vfs = tiledb.VFS()
buffer = b"0123456789"
with tiledb.FileIO(vfs, self.path("foo"), mode="wb") as fio:
fio.write(buffer)
fio.flush()
self.assertEqual(fio.tell(), len(buffer))
with tiledb.FileIO(vfs, self.path("foo"), mode="rb") as fio:
with self.assertRaises(IOError):
fio.write(b"foo")
self.assertEqual(vfs.file_size(self.path("foo")), len(buffer))
fio = tiledb.FileIO(vfs, self.path("foo"), mode="rb")
self.assertEqual(fio.read(3), b"012")
self.assertEqual(fio.tell(), 3)
self.assertEqual(fio.read(3), b"345")
self.assertEqual(fio.tell(), 6)
self.assertEqual(fio.read(10), b"6789")
self.assertEqual(fio.tell(), 10)
# seek from beginning
fio.seek(0)
self.assertEqual(fio.tell(), 0)
self.assertEqual(fio.read(), buffer)
# seek must be positive when SEEK_SET
with self.assertRaises(ValueError):
fio.seek(-1, 0)
# seek from current positfion
fio.seek(5)
self.assertEqual(fio.tell(), 5)
fio.seek(3, 1)
self.assertEqual(fio.tell(), 8)
fio.seek(-3, 1)
self.assertEqual(fio.tell(), 5)
# seek from end
fio.seek(-4, 2)
self.assertEqual(fio.tell(), 6)
# Test readall
fio.seek(0)
self.assertEqual(fio.readall(), buffer)
self.assertEqual(fio.tell(), 10)
fio.seek(5)
self.assertEqual(fio.readall(), buffer[5:])
self.assertEqual(fio.readall(), b"")
# Test readinto
fio.seek(0)
test_bytes = bytearray(10)
self.assertEqual(fio.readinto(test_bytes), 10)
self.assertEqual(test_bytes, buffer)
# Reading from the end should return empty
fio.seek(0)
fio.read()
self.assertEqual(fio.read(), b"")
# Test writing and reading lines with TextIOWrapper
lines = [rand_utf8(random.randint(0, 50)) + "\n" for _ in range(10)]
rand_uri = self.path("test_fio.rand")
with tiledb.FileIO(vfs, rand_uri, "wb") as f:
txtio = io.TextIOWrapper(f, encoding="utf-8")
txtio.writelines(lines)
txtio.flush()
with tiledb.FileIO(vfs, rand_uri, "rb") as f2:
txtio = io.TextIOWrapper(f2, encoding="utf-8")
self.assertEqual(txtio.readlines(), lines)
def test_sc42569_vfs_memoryview(self):
# This test is to ensure that giving np.ndarray buffer to readinto works
# when trying to write bytes that cannot be converted to float32 or int32
vfs = tiledb.VFS()
buffer = b"012\x00\x01"
with tiledb.FileIO(vfs, self.path("foo"), mode="wb") as fio:
fio.write(buffer)
fio.flush()
self.assertEqual(fio.tell(), len(buffer))
fio = tiledb.FileIO(vfs, self.path("foo"), mode="rb")
# Test readinto with np.float32
fio.seek(0)
test_np_array = np.empty(5, dtype=np.float32)
n_bytes = fio.readinto(test_np_array)
self.assertEqual(n_bytes, 5)
self.assertEqual(test_np_array.tobytes()[:n_bytes], buffer)
# Test readinto with np.int32
fio.seek(0)
test_np_array = np.empty(5, dtype=np.int32)
n_bytes = fio.readinto(test_np_array)
self.assertEqual(n_bytes, 5)
self.assertEqual(test_np_array.tobytes()[:n_bytes], buffer)
def test_ls(self):
basepath = self.path("test_vfs_ls")
self.vfs.create_dir(basepath)
for id in (1, 2, 3):
dir = os.path.join(basepath, f"dir{id}")
self.vfs.create_dir(dir)
fname = os.path.join(basepath, "file_" + str(id))
with tiledb.FileIO(self.vfs, fname, "wb") as fio:
fio.write(b"")
expected = ("file_1", "file_2", "file_3")
# empty directories do not "exist" on s3
if pytest.tiledb_vfs != "s3":
expected = expected + ("dir1", "dir2", "dir3")
self.assertSetEqual(
set(expected),
set(
map(
lambda x: os.path.basename(x.split("test_vfs_ls")[1]),
self.vfs.ls(basepath),
)
),
)
@pytest.mark.skipif(
pytest.tiledb_vfs not in ["file", "s3", "azure", "gcs"],
reason="Only test on local, S3, Azure, and GCS",
)
def test_ls_recursive(self):
# Create a nested directory structure to test recursive listing
basepath = self.path("test_vfs_ls_recursive")
self.vfs.create_dir(basepath)
dir = os.path.join(basepath, "dir1")
self.vfs.create_dir(dir)
fname = os.path.join(dir, "file_1")
with tiledb.FileIO(self.vfs, fname, "wb") as fio:
fio.write(b"")
fname = os.path.join(dir, "file_2")
with tiledb.FileIO(self.vfs, fname, "wb") as fio:
fio.write(b"")
dir = os.path.join(basepath, "dir2")
self.vfs.create_dir(dir)
dir2 = os.path.join(dir, "dir2_1")
self.vfs.create_dir(dir2)
fname = os.path.join(dir2, "file_1")
with tiledb.FileIO(self.vfs, fname, "wb") as fio:
fio.write(b"")
fname = os.path.join(dir2, "file_2")
with tiledb.FileIO(self.vfs, fname, "wb") as fio:
fio.write(b"")
dir2 = os.path.join(dir, "dir2_2")
self.vfs.create_dir(dir2)
fname = os.path.join(dir2, "file_1")
with tiledb.FileIO(self.vfs, fname, "wb") as fio:
fio.write(b"")
expected = [
"dir1",
"dir1/file_1",
"dir1/file_2",
"dir2",
"dir2/dir2_1",
"dir2/dir2_1/file_1",
"dir2/dir2_1/file_2",
"dir2/dir2_2",
"dir2/dir2_2/file_1",
]
self.assertSetEqual(
set(expected),
set(
map(
# # Keep only the paths after the basepath and normalize them to work on all platforms
lambda x: os.path.normpath(
x.split("test_vfs_ls_recursive/")[1]
).replace("\\", "/"),
self.vfs.ls_recursive(basepath),
)
),
)
# Check with user provided callback
callback_results = []
def callback(uri, _): # we don't use the second argument 'is_dir'
callback_results.append(uri)
return True
self.vfs.ls_recursive(basepath, callback)
self.assertSetEqual(
set(expected),
set(
map(
# Keep only the paths after the basepath and normalize them to work on all platforms
lambda x: os.path.normpath(
x.split("test_vfs_ls_recursive/")[1]
).replace("\\", "/"),
callback_results,
)
),
)
# Can also be called by calling ls with recursive=True
self.assertSetEqual(
set(expected),
set(
map(
# Keep only the paths after the basepath and normalize them to work on all platforms
lambda x: os.path.normpath(
x.split("test_vfs_ls_recursive/")[1]
).replace("\\", "/"),
self.vfs.ls(basepath, recursive=True),
)
),
)
def test_dir_size(self):
vfs = tiledb.VFS()
path = self.path("test_vfs_dir_size")
vfs.create_dir(path)
rand_sizes = np.random.choice(100, size=4, replace=False)
for size in rand_sizes:
file_path = os.path.join(path, "f_" + str(size))
with tiledb.FileIO(vfs, file_path, "wb") as f:
data = os.urandom(size)
f.write(data)
self.assertEqual(vfs.dir_size(path), sum(rand_sizes))
def test_open_with(self):
uri = self.path("test_open_with")
vfs = tiledb.VFS()
buffer = b"0123456789"
with vfs.open(uri, mode="wb") as fio:
fio.write(buffer)
fio.flush()
self.assertEqual(fio.tell(), len(buffer))
with vfs.open(uri, mode="rb") as fio:
with self.assertRaises(IOError):
fio.write(b"foo")
self.assertEqual(fio.read(len(buffer)), buffer)
def test_vfs_isdir(tmp_path):
"""isdir is an alias for is_dir."""
fs = tiledb.VFS()
assert fs.isdir(tmp_path.as_posix())
def test_vfs_isfile(tmp_path):
"""isfile is an alias for is_file."""
tmp_file = tmp_path.joinpath("foo")
tmp_file.touch()
fs = tiledb.VFS()
assert fs.isfile(tmp_file.as_posix())
def test_vfs_size(tmp_path):
"""size is an alias for file_size."""
tmp_file = tmp_path.joinpath("foo")
buffer = b"0123456789"
tmp_file.write_bytes(buffer)
fs = tiledb.VFS()
assert fs.size(tmp_file.as_posix()) == len(buffer)
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