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import io
import mmap
import numpy as np
import pytest
from asdf import constants, generic_io
from asdf._block import io as bio
from asdf._block.exceptions import BlockIndexError
def test_checksum(tmp_path):
my_array = np.arange(0, 64, dtype="<i8")
target_checksum = b"\xcaM\\\xb8t_L|\x00\n+\x01\xf1\xcfP1"
assert bio.calculate_block_checksum(my_array) == target_checksum
assert bio.calculate_block_checksum(my_array.reshape((8, 8))) == target_checksum
# check that when written, a block generates the correct checksum
path = tmp_path / "test"
with generic_io.get_file(path, mode="w") as fd:
bio.write_block(fd, my_array.view(dtype="uint8"))
with generic_io.get_file(path, mode="r") as fd:
_, header, _, _ = bio.read_block(fd)
assert header["checksum"] == target_checksum
def test_validate_block_header():
# check for invalid compression
with pytest.raises(ValueError):
bio.validate_block_header({"compression": b"foo"})
# streamed blocks cannot be compressed
with pytest.raises(ValueError):
bio.validate_block_header({"compression": b"zlib", "flags": constants.BLOCK_FLAG_STREAMED})
bio.validate_block_header(
{"compression": b"\0\0\0\0", "flags": constants.BLOCK_FLAG_STREAMED, "used_size": 0, "data_size": 0},
)
# if not compressed, used_size must equal data_size
with pytest.raises(ValueError):
bio.validate_block_header({"compression": b"\0\0\0\0", "flags": 0, "used_size": 1, "data_size": 0})
bio.validate_block_header({"compression": b"zlib", "flags": 0, "used_size": 1, "data_size": 0})
def test_read_block_header(tmp_path):
# first write out a file with a block
my_array = np.arange(0, 64, dtype="<i8")
path = tmp_path / "test"
with generic_io.get_file(path, mode="w") as fd:
written_header = bio.write_block(fd, my_array.view("uint8"))
# try reading the block header at the start
with generic_io.get_file(path, mode="r") as fd:
header = bio.read_block_header(fd)
assert header == written_header
# seek into the header, creating an invalid starting position
# where the header size will be 0
with generic_io.get_file(path, mode="r") as fd:
fd.seek(10)
with pytest.raises(ValueError):
header = bio.read_block_header(fd)
# check that offset, when provided is used
with generic_io.get_file(path, mode="r") as fd, pytest.raises(ValueError):
header = bio.read_block_header(fd, offset=10)
with generic_io.get_file(path, mode="r") as fd:
fd.seek(4)
header = bio.read_block_header(fd, offset=0)
assert header == written_header
def test_read_block_data(tmp_path):
# first write out a file with a block
my_array = np.arange(0, 64, dtype="uint8")
path = tmp_path / "test"
with generic_io.get_file(path, mode="w") as fd:
bio.write_block(fd, my_array)
# read the header and get the offset within the file where the
# data is located
with generic_io.get_file(path, mode="r") as fd:
header = bio.read_block_header(fd)
data_offset = fd.tell()
data = bio.read_block_data(fd, header)
assert np.array_equal(data, my_array)
# check that offset works as expected
data = bio.read_block_data(fd, header, offset=data_offset)
assert np.array_equal(data, my_array)
# not lazy loaded, memmapped
with generic_io.get_file(path, mode="r") as fd:
offset, header, read_data_offset, data = bio.read_block(fd, lazy_load=False, memmap=True)
assert offset == 0
assert read_data_offset == data_offset
assert np.array_equal(data, my_array)
base = data
while getattr(base, "base", None) is not None:
base = base.base
assert isinstance(base, mmap.mmap)
# not memmapped, lazy
with generic_io.get_file(path, mode="r") as fd:
offset, header, read_data_offset, data = bio.read_block(fd, lazy_load=True, memmap=False)
assert offset == 0
assert read_data_offset == data_offset
assert np.array_equal(data(), my_array)
base = data()
while getattr(base, "base", None) is not None:
base = base.base
assert not isinstance(base, mmap.mmap)
def test_read_block(tmp_path):
block_bytes = io.BytesIO(
b"\x000" # header size = 2
+ b"\0\0\0\0" # flags = 4
+ b"\0\0\0\0" # compression = 4
+ b"\0\0\0\0\0\0\0\0" # allocated size = 8
+ b"\0\0\0\0\0\0\0\0" # used size = 8
+ b"\0\0\0\0\0\0\0\0" # data size = 8
+ b"\xd4\x1d\x8c\xd9\x8f\x00\xb2\x04\xe9\x80\t\x98\xec\xf8B~", # checksum = 16
)
with generic_io.get_file(block_bytes, mode="r") as fd:
offset, header, data_offset, data = bio.read_block(fd)
assert offset == 0
assert data_offset == 50
assert len(data) == 0
for k in "flags", "allocated_size", "used_size", "data_size":
assert header[k] == 0
def test_write_block(tmp_path):
expected = (
b"\x000" # header size = 2
+ b"\0\0\0\0" # flags
+ b"\0\0\0\0" # compression
+ b"\0\0\0\0\0\0\0\0" # allocated size
+ b"\0\0\0\0\0\0\0\0" # used size
+ b"\0\0\0\0\0\0\0\0" # data size
+ b"\xd4\x1d\x8c\xd9\x8f\x00\xb2\x04\xe9\x80\t\x98\xec\xf8B~" # checksum
)
# first write out a file with a block
my_array = np.array([], dtype="uint8")
path = tmp_path / "test"
with generic_io.get_file(path, mode="w") as fd:
bio.write_block(fd, my_array)
with generic_io.get_file(path, mode="r") as fd:
buff = fd.read(-1)
assert buff == expected
def test_write_block_offset():
data = np.ones(30, dtype="uint8")
raw_fd = io.BytesIO()
fd = generic_io.get_file(raw_fd, mode="rw")
fd.write(b"0000000")
bio.write_block(fd, data, offset=0)
fd.seek(0)
_, _, _, d = bio.read_block(fd)
np.testing.assert_array_equal(data, d)
def test_write_oversized_block():
# check that writing does not occur if data_size > allocated_size
data = np.ones(30, dtype="uint8")
raw_fd = io.BytesIO()
fd = generic_io.get_file(raw_fd, mode="rw")
with pytest.raises(RuntimeError, match="Block used size.*"):
bio.write_block(fd, data, allocated_size=0)
assert fd.tell() == 0
def test_fd_not_seekable():
data = np.ones(30, dtype="uint8")
raw_fd = io.BytesIO()
fd = generic_io.get_file(raw_fd, mode="rw")
bio.write_block(fd, data)
raw_fd.seek(0)
fd = generic_io.get_file(raw_fd, mode="rw")
seekable = lambda: False # noqa: E731
fd.seekable = seekable
_, _, _, d = bio.read_block(fd)
np.testing.assert_array_equal(d, data)
with pytest.raises(ValueError, match="write_block received offset.*"):
bio.write_block(fd, data, offset=0)
def test_compressed_block():
data = np.ones(30, dtype="uint8")
fd = generic_io.get_file(io.BytesIO(), mode="rw")
write_header = bio.write_block(fd, data, compression="zlib")
assert write_header["compression"] == b"zlib"
_, _, _, rdata = bio.read_block(fd, offset=0)
np.testing.assert_array_equal(rdata, data)
def test_stream_block():
data = np.ones(10, dtype="uint8")
fd = generic_io.get_file(io.BytesIO(), mode="rw")
write_header = bio.write_block(fd, data, stream=True)
assert write_header["flags"] & constants.BLOCK_FLAG_STREAMED
# now write extra data to file
extra_data = np.ones(10, dtype="uint8")
fd.write_array(extra_data)
_, _, _, rdata = bio.read_block(fd, offset=0)
assert rdata.size == 20
assert np.all(rdata == 1)
def test_read_from_closed(tmp_path):
fn = tmp_path / "test.blk"
data = np.ones(10, dtype="uint8")
with generic_io.get_file(fn, mode="w") as fd:
bio.write_block(fd, data, stream=True)
with generic_io.get_file(fn, mode="rw") as fd:
_, _, _, callback = bio.read_block(fd, offset=0, lazy_load=True)
with pytest.raises(OSError, match="ASDF file has already been closed. Can not get the data."):
callback()
@pytest.mark.parametrize("data", [np.ones(10, dtype="f4"), np.ones((3, 3), dtype="uint8")])
def test_invalid_data(data):
fd = generic_io.get_file(io.BytesIO(), mode="rw")
with pytest.raises(ValueError, match="Data must be of.*"):
bio.write_block(fd, data, stream=True)
@pytest.mark.parametrize(
"options",
[
(0, 10, 5, [5, 0]),
(0, 10, 3, [9, 6, 3, 0]),
(0, 10, 10, [0]),
(0, 10, 6, [6, 0]),
(0, 10, 11, [0]),
(0, 10, 4096, [0]),
],
)
def test_candidate_offsets(options):
min_offset, max_offset, size, targets = options
for offset, target in zip(bio._candidate_offsets(min_offset, max_offset, size), targets):
assert offset == target
def generate_block_index_file(fn, values=None, offset=0):
if values is None:
values = [1, 2, 3]
with generic_io.get_file(fn, "w") as f:
f.write(b"\0" * offset)
bio.write_block_index(f, values)
def test_find_block_index(tmp_path):
offset = 42
fn = tmp_path / "test"
generate_block_index_file(fn, offset=offset)
with generic_io.get_file(fn, "r") as fd:
assert bio.find_block_index(fd) == offset
def test_find_block_index_on_boundry(tmp_path):
fn = tmp_path / "test"
with generic_io.get_file(fn, "w") as fd:
block_size = fd.block_size
# put pattern across a block boundary
offset = block_size - (len(constants.INDEX_HEADER) // 2)
generate_block_index_file(fn, offset=offset)
with generic_io.get_file(fn, "r") as fd:
assert bio.find_block_index(fd) == offset
def test_missing_block_index(tmp_path):
fn = tmp_path / "test"
with open(fn, "w") as f:
f.write("\0" * 4096)
with generic_io.get_file(fn, "r") as fd:
assert bio.find_block_index(fd) is None
def test_less_than_min_offset_block_index(tmp_path):
fn = tmp_path / "test"
offset = 26
min_offset = 42
generate_block_index_file(fn, offset=offset)
with generic_io.get_file(fn, "r") as fd:
assert bio.find_block_index(fd, min_offset) is None
def test_greater_than_max_offset_block_index(tmp_path):
fn = tmp_path / "test"
offset = 72
max_offset = 42
generate_block_index_file(fn, offset=offset)
with generic_io.get_file(fn, "r") as fd:
assert bio.find_block_index(fd, 0, max_offset) is None
def test_read_block_index(tmp_path):
fn = tmp_path / "test"
values = [1, 2, 3]
generate_block_index_file(fn, values=values, offset=0)
with generic_io.get_file(fn, "r") as fd:
assert bio.read_block_index(fd) == values
def test_read_block_index_with_offset(tmp_path):
fn = tmp_path / "test"
values = [1, 2, 3]
offset = 42
generate_block_index_file(fn, values=values, offset=offset)
with generic_io.get_file(fn, "r") as fd:
assert bio.read_block_index(fd, offset) == values
def test_read_block_index_pre_seek(tmp_path):
fn = tmp_path / "test"
values = [1, 2, 3]
offset = 42
generate_block_index_file(fn, values=values, offset=offset)
with generic_io.get_file(fn, "r") as fd:
fd.seek(offset)
assert bio.read_block_index(fd) == values
def test_read_block_index_no_header(tmp_path):
fn = tmp_path / "test"
values = [1, 2, 3]
generate_block_index_file(fn, values=values, offset=0)
with generic_io.get_file(fn, "r") as fd:
fd.seek(len(constants.INDEX_HEADER))
with pytest.raises(BlockIndexError, match="Failed to read block index.*"):
assert bio.read_block_index(fd) == values
def test_read_block_index_invalid_yaml():
bs = io.BytesIO(constants.INDEX_HEADER + b"][")
with generic_io.get_file(bs, "r") as fd:
with pytest.raises(BlockIndexError, match="Failed to parse block index as yaml"):
bio.read_block_index(fd)
def test_read_block_index_valid_yaml_invalid_contents():
bs = io.BytesIO(constants.INDEX_HEADER + b"['a', 'b']")
with generic_io.get_file(bs, "r") as fd:
with pytest.raises(BlockIndexError, match="Invalid block index"):
bio.read_block_index(fd)
def test_write_block_index_with_offset(tmp_path):
fn = tmp_path / "test"
offset = 50
with generic_io.get_file(fn, "w") as fd:
fd.write(b"\0" * 100)
fd.seek(0)
bio.write_block_index(fd, [1, 2, 3], offset=offset)
with generic_io.get_file(fn, "r") as fd:
assert bio.find_block_index(fd) == offset
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