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"""
Tests for the xopen.xopen function
"""
import bz2
from contextlib import contextmanager
import functools
import gzip
import io
import itertools
import lzma
import os
from pathlib import Path
import shutil
import pytest
from xopen import xopen, _detect_format_from_content
try:
import zstandard
except ImportError:
zstandard = None
# TODO this is duplicated in test_piped.py
TEST_DIR = Path(__file__).parent
CONTENT_LINES = ["Testing, testing ...\n", "The second line.\n"]
CONTENT = "".join(CONTENT_LINES)
extensions = ["", ".gz", ".bz2", ".xz"]
if shutil.which("zstd") or zstandard:
extensions += [".zst"]
base = os.path.join(os.path.dirname(__file__), "file.txt")
files = [base + ext for ext in extensions]
@contextmanager
def disable_binary(tmp_path, binary_name):
"""
Find the location of the binary by its name, then set PATH to a directory that contains
the binary with permissions set to 000. If no suitable binary could be found,
PATH is set to an empty directory
"""
binary_path = shutil.which(binary_name)
if binary_path:
shutil.copy(binary_path, tmp_path)
os.chmod(tmp_path / Path(binary_path).name, 0)
path = os.environ["PATH"]
try:
os.environ["PATH"] = str(tmp_path)
yield
finally:
os.environ["PATH"] = path
@pytest.fixture(params=extensions)
def ext(request):
return request.param
@pytest.fixture(params=files)
def fname(request):
return request.param
@pytest.fixture
def lacking_pigz_permissions(tmp_path):
with disable_binary(tmp_path, "pigz"):
yield
@pytest.fixture
def lacking_pbzip2_permissions(tmp_path):
with disable_binary(tmp_path, "pbzip2"):
yield
@pytest.fixture
def lacking_xz_permissions(tmp_path):
with disable_binary(tmp_path, "xz"):
yield
@pytest.fixture
def xopen_without_igzip(monkeypatch):
import xopen # xopen local overrides xopen global variable
monkeypatch.setattr(xopen, "igzip", None)
return xopen.xopen
def test_text(fname):
with xopen(fname, "rt") as f:
lines = list(f)
assert len(lines) == 2
assert lines[1] == "The second line.\n", fname
def test_binary(fname):
with xopen(fname, "rb") as f:
lines = list(f)
assert len(lines) == 2
assert lines[1] == b"The second line.\n", fname
@pytest.mark.parametrize("mode", ["b", "", "t"])
@pytest.mark.parametrize("threads", [None, 0])
def test_roundtrip(ext, tmp_path, threads, mode):
if ext == ".zst" and threads == 0 and zstandard is None:
return
path = tmp_path / f"file{ext}"
data = b"Hello" if mode == "b" else "Hello"
with xopen(path, "w" + mode, threads=threads) as f:
f.write(data)
with xopen(path, "r" + mode, threads=threads) as f:
assert f.read() == data
def test_binary_no_isal_no_threads(fname, xopen_without_igzip):
if fname.endswith(".zst") and zstandard is None:
return
with xopen_without_igzip(fname, "rb", threads=0) as f:
lines = list(f)
assert len(lines) == 2
assert lines[1] == b"The second line.\n", fname
def test_binary_no_isal(fname, xopen_without_igzip):
with xopen_without_igzip(fname, "rb", threads=1) as f:
lines = list(f)
assert len(lines) == 2
assert lines[1] == b"The second line.\n", fname
def test_no_context_manager_text(fname):
f = xopen(fname, "rt")
lines = list(f)
assert len(lines) == 2
assert lines[1] == "The second line.\n", fname
f.close()
assert f.closed
def test_no_context_manager_binary(fname):
f = xopen(fname, "rb")
lines = list(f)
assert len(lines) == 2
assert lines[1] == b"The second line.\n", fname
f.close()
assert f.closed
def test_bytes_path(fname):
path = fname.encode("utf-8")
with xopen(path, "rt") as f:
lines = list(f)
assert len(lines) == 2
assert lines[1] == "The second line.\n", fname
def test_readinto(fname):
content = CONTENT.encode("utf-8")
with xopen(fname, "rb") as f:
b = bytearray(len(content) + 100)
length = f.readinto(b)
assert length == len(content)
assert b[:length] == content
def test_detect_format_from_content(ext):
detected = _detect_format_from_content(Path(__file__).parent / f"file.txt{ext}")
if ext == "":
assert detected is None
else:
assert ext[1:] == detected
def test_detect_file_format_from_content(ext, tmp_path):
path = tmp_path / f"file.txt{ext}.test"
shutil.copy(TEST_DIR / f"file.txt{ext}", path)
with xopen(path, "rb") as fh:
assert fh.readline() == CONTENT_LINES[0].encode("utf-8")
def test_readline(fname):
first_line = CONTENT_LINES[0].encode("utf-8")
with xopen(fname, "rb") as f:
assert f.readline() == first_line
def test_readline_text(fname):
with xopen(fname, "r") as f:
assert f.readline() == CONTENT_LINES[0]
def test_next(fname):
with xopen(fname, "rt") as f:
_ = next(f)
line2 = next(f)
assert line2 == "The second line.\n", fname
def test_has_iter_method(ext, tmp_path):
path = tmp_path / f"out{ext}"
with xopen(path, mode="w") as f:
# Writing anything isn’t strictly necessary, but if we don’t, then
# pbzip2 causes a delay of one second
f.write("hello")
assert hasattr(f, "__iter__")
def test_iter_without_with(fname):
f = xopen(fname, "rt")
it = iter(f)
assert CONTENT_LINES[0] == next(it)
f.close()
@pytest.mark.parametrize("extension", [".gz", ".bz2"])
def test_partial_iteration_closes_correctly(extension, create_large_file):
class LineReader:
def __init__(self, file):
self.file = xopen(file, "rb")
def __iter__(self):
wrapper = io.TextIOWrapper(self.file, encoding="utf-8")
yield from wrapper
large_file = create_large_file(extension)
f = LineReader(large_file)
next(iter(f))
f.file.close()
def test_nonexisting_file(ext):
with pytest.raises(IOError):
with xopen("this-file-does-not-exist" + ext):
pass # pragma: no cover
def test_write_to_nonexisting_dir(ext):
with pytest.raises(IOError):
with xopen("this/path/does/not/exist/file.txt" + ext, "w"):
pass # pragma: no cover
def test_invalid_mode(ext):
with pytest.raises(ValueError):
with xopen(TEST_DIR / f"file.txt.{ext}", mode="hallo"):
pass # pragma: no cover
def test_filename_not_a_string():
with pytest.raises(TypeError):
with xopen(123, mode="r"):
pass # pragma: no cover
def test_invalid_compression_level(tmp_path):
with pytest.raises(ValueError) as e:
with xopen(tmp_path / "out.gz", mode="w", compresslevel=17) as f:
f.write("hello") # pragma: no cover
assert "compresslevel must be" in e.value.args[0]
@pytest.mark.parametrize("ext", extensions)
def test_append(ext, tmp_path):
text = b"AB"
reference = text + text
path = tmp_path / f"the-file{ext}"
with xopen(path, "ab") as f:
f.write(text)
with xopen(path, "ab") as f:
f.write(text)
with xopen(path, "r") as f:
for appended in f:
pass
reference = reference.decode("utf-8")
assert appended == reference
@pytest.mark.parametrize("ext", extensions)
def test_append_text(ext, tmp_path):
text = "AB"
reference = text + text
path = tmp_path / f"the-file{ext}"
with xopen(path, "at") as f:
f.write(text)
with xopen(path, "at") as f:
f.write(text)
with xopen(path, "rt") as f:
for appended in f:
pass
assert appended == reference
@pytest.mark.timeout(15)
@pytest.mark.parametrize("extension", [".gz", ".bz2", ".xz"])
def test_truncated_file(extension, create_truncated_file):
truncated_file = create_truncated_file(extension)
with pytest.raises((EOFError, IOError)):
f = xopen(truncated_file, "r")
f.read()
f.close() # pragma: no cover
@pytest.mark.timeout(15)
@pytest.mark.parametrize("extension", [".gz", ".bz2", ".xz"])
def test_truncated_iter(extension, create_truncated_file):
truncated_file = create_truncated_file(extension)
with pytest.raises((EOFError, IOError)):
f = xopen(truncated_file, "r")
for line in f:
pass
f.close() # pragma: no cover
@pytest.mark.timeout(15)
@pytest.mark.parametrize("extension", [".gz", ".bz2", ".xz"])
def test_truncated_with(extension, create_truncated_file):
truncated_file = create_truncated_file(extension)
with pytest.raises((EOFError, IOError)):
with xopen(truncated_file, "r") as f:
f.read()
@pytest.mark.timeout(15)
@pytest.mark.parametrize("extension", [".gz", ".bz2", ".xz"])
def test_truncated_iter_with(extension, create_truncated_file):
truncated_file = create_truncated_file(extension)
with pytest.raises((EOFError, IOError)):
with xopen(truncated_file, "r") as f:
for line in f:
pass
def test_bare_read_from_gz():
hello_file = TEST_DIR / "hello.gz"
with xopen(hello_file, "rt") as f:
assert f.read() == "hello"
def test_read_no_threads(ext):
klasses = {
".bz2": bz2.BZ2File,
".gz": gzip.GzipFile,
".xz": lzma.LZMAFile,
".zst": io.BufferedReader,
"": io.BufferedReader,
}
if ext == ".zst" and zstandard is None:
return
klass = klasses[ext]
with xopen(TEST_DIR / f"file.txt{ext}", "rb", threads=0) as f:
assert isinstance(f, klass), f
def test_write_threads(tmp_path, ext):
path = tmp_path / f"out.{ext}"
with xopen(path, mode="w", threads=3) as f:
f.write("hello")
with xopen(path) as f:
assert f.read() == "hello"
def test_write_pigz_threads_no_isal(tmp_path, xopen_without_igzip):
path = tmp_path / "out.gz"
with xopen_without_igzip(path, mode="w", threads=3) as f:
f.write("hello")
with xopen_without_igzip(path) as f:
assert f.read() == "hello"
def test_write_no_threads(tmp_path, ext):
klasses = {
".bz2": bz2.BZ2File,
".gz": gzip.GzipFile,
".xz": lzma.LZMAFile,
"": io.BufferedWriter,
}
if ext == ".zst":
# Skip zst because if python-zstandard is not installed,
# we fall back to an external process even when threads=0
return
klass = klasses[ext]
with xopen(tmp_path / f"out{ext}", "wb", threads=0) as f:
assert isinstance(f, io.BufferedWriter)
if ext:
assert isinstance(f.raw, klass), f
def test_write_gzip_no_threads_no_isal(tmp_path, xopen_without_igzip):
import gzip
with xopen_without_igzip(tmp_path / "out.gz", "wb", threads=0) as f:
assert isinstance(f.raw, gzip.GzipFile), f
def test_write_stdout():
f = xopen("-", mode="w")
print("Hello", file=f)
f.close()
# ensure stdout is not closed
print("Still there?")
def test_write_stdout_contextmanager():
# Do not close stdout
with xopen("-", mode="w") as f:
print("Hello", file=f)
# ensure stdout is not closed
print("Still there?")
def test_read_pathlib(fname):
path = Path(fname)
with xopen(path, mode="rt") as f:
assert f.read() == CONTENT
def test_read_pathlib_binary(fname):
path = Path(fname)
with xopen(path, mode="rb") as f:
assert f.read() == bytes(CONTENT, "ascii")
def test_write_pathlib(ext, tmp_path):
path = tmp_path / f"hello.txt{ext}"
with xopen(path, mode="wt") as f:
f.write("hello")
with xopen(path, mode="rt") as f:
assert f.read() == "hello"
def test_write_pathlib_binary(ext, tmp_path):
path = tmp_path / f"hello.txt{ext}"
with xopen(path, mode="wb") as f:
f.write(b"hello")
with xopen(path, mode="rb") as f:
assert f.read() == b"hello"
def test_falls_back_to_gzip_open(lacking_pigz_permissions):
with xopen(TEST_DIR / "file.txt.gz", "rb") as f:
assert f.readline() == CONTENT_LINES[0].encode("utf-8")
def test_falls_back_to_gzip_open_no_isal(lacking_pigz_permissions, xopen_without_igzip):
with xopen_without_igzip(TEST_DIR / "file.txt.gz", "rb") as f:
assert f.readline() == CONTENT_LINES[0].encode("utf-8")
def test_fals_back_to_gzip_open_write_no_isal(
lacking_pigz_permissions, xopen_without_igzip, tmp_path
):
tmp = tmp_path / "test.gz"
with xopen_without_igzip(tmp, "wb") as f:
f.write(b"hello")
assert gzip.decompress(tmp.read_bytes()) == b"hello"
def test_falls_back_to_bzip2_open(lacking_pbzip2_permissions):
with xopen(TEST_DIR / "file.txt.bz2", "rb") as f:
assert f.readline() == CONTENT_LINES[0].encode("utf-8")
def test_falls_back_to_lzma_open(lacking_xz_permissions):
with xopen(TEST_DIR / "file.txt.xz", "rb") as f:
assert f.readline() == CONTENT_LINES[0].encode("utf-8")
def test_open_many_writers(tmp_path, ext):
files = []
# Because lzma.open allocates a lot of memory,
# open fewer files to avoid MemoryError on 32-bit architectures
n = 21 if ext == ".xz" else 61
for i in range(1, n):
path = tmp_path / f"{i:03d}.txt{ext}"
f = xopen(path, "wb", threads=2)
f.write(b"hello")
files.append(f)
for f in files:
f.close()
def test_override_output_format(tmp_path):
path = tmp_path / "test_gzip_compressed"
with xopen(path, mode="wb", format="gz") as f:
f.write(b"test")
test_contents = path.read_bytes()
assert test_contents.startswith(b"\x1f\x8b") # Gzip magic
assert gzip.decompress(test_contents) == b"test"
def test_override_output_format_unsupported_format(tmp_path):
path = tmp_path / "test_fairy_format_compressed"
with pytest.raises(ValueError) as error:
xopen(path, mode="wb", format="fairy")
error.match("not supported")
error.match("fairy")
def test_override_output_format_wrong_format(tmp_path):
path = tmp_path / "not_compressed"
path.write_text("I am not compressed.", encoding="utf-8")
with pytest.raises(OSError): # BadGzipFile is a subclass of OSError
with xopen(path, "rt", format="gz") as opened_file:
opened_file.read()
# Test for threaded and non-threaded.
OPENERS = (xopen, functools.partial(xopen, threads=0))
@pytest.mark.parametrize(
["opener", "extension"], itertools.product(OPENERS, extensions)
)
def test_text_encoding_newline_passthrough(opener, extension, tmp_path):
if extension == ".zst" and zstandard is None:
return
# "Eén ree\nTwee reeën\n" latin-1 encoded with \r for as line separator.
encoded_text = b"E\xe9n ree\rTwee ree\xebn\r"
path = tmp_path / f"test.txt{extension}"
with opener(path, "wb") as f:
f.write(encoded_text)
with opener(path, "rt", encoding="latin-1", newline="\r") as f:
result = f.read()
assert result == "Eén ree\rTwee reeën\r"
@pytest.mark.parametrize(
["opener", "extension"], itertools.product(OPENERS, extensions)
)
def test_text_encoding_errors(opener, extension, tmp_path):
if extension == ".zst" and zstandard is None:
return
# "Eén ree\nTwee reeën\n" latin-1 encoded. This is not valid ascii.
encoded_text = b"E\xe9n ree\nTwee ree\xebn\n"
path = tmp_path / f"test.txt{extension}"
with opener(path, "wb") as f:
f.write(encoded_text)
with opener(path, "rt", encoding="ascii", errors="replace") as f:
result = f.read()
assert result == "E�n ree\nTwee ree�n\n"
@pytest.mark.parametrize("compresslevel", [1, 6])
def test_gzip_compression_is_reproducible_without_piping(tmp_path, compresslevel):
# compresslevel 1 should give us igzip and 6 should give us regular gzip
path = tmp_path / "test.gz"
with xopen(path, mode="wb", compresslevel=compresslevel, threads=0) as f:
f.write(b"hello")
data = path.read_bytes()
assert (data[3] & gzip.FNAME) == 0, "gzip header contains file name"
assert data[4:8] == b"\0\0\0\0", "gzip header contains mtime"
def test_read_devnull():
with xopen(os.devnull):
pass
def test_xopen_zst_fails_when_zstandard_not_available(monkeypatch):
import xopen
monkeypatch.setattr(xopen, "zstandard", None)
with pytest.raises(ImportError):
with xopen.xopen(TEST_DIR / "file.txt.zst", mode="rb", threads=0) as f:
f.read()
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