def test_appending():
"""appending to an existing logfile should work"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = LOGFILE_NAME
LOGGER.input_file("sample.fasta")
LOGGER.shutdown()
records = Counter()
with open(LOGFILE_NAME) as infile:
for line in infile:
records[line] += 1
vals = set(list(records.values()))
assert vals == {1}
LOGGER = CachingLogger(create_dir=True)
LOGGER.mode = "a"
LOGGER.log_file_path = LOGFILE_NAME
LOGGER.input_file("sample.fasta")
LOGGER.shutdown()
records = Counter()
with open(LOGFILE_NAME) as infile:
for line in infile:
records[line] += 1
vals = set(list(records.values()))
assert vals == {2}
try:
os.remove(LOGFILE_NAME)
except OSError:
pass
def test_set_path_if_exists():
"""cannot change an existing logging path"""
with TemporaryDirectory(dir=".") as dirname:
dirname = Path(dirname)
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = dirname / LOGFILE_NAME
LOGGER.input_file(TEST_ROOTDIR / "sample-lf.fasta")
with pytest.raises(AttributeError):
LOGGER.log_file_path = dirname / "invalid.log"
LOGGER.shutdown()
def test_mdsum_output():
"""md5 sum of output file should be correct"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = LOGFILE_NAME
# first file has LF, second has CRLF line endings
hex_path = [
("96eb2c2632bae19eb65ea9224aaafdad", "sample-lf.fasta"),
]
LOGGER.output_file(TEST_ROOTDIR / "sample-lf.fasta")
LOGGER.shutdown()
with open(LOGFILE_NAME, "r") as infile:
num = 0
for line in infile:
for h, p in hex_path:
if p in line:
line = next(infile)
assert h in line
num += 1
assert num == len(hex_path)
try:
shutil.rmtree(DIRNAME)
except OSError:
pass
def test_shutdown():
"""correctly purges contents"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = LOGFILE_NAME
LOGGER.input_file(TEST_ROOTDIR / "sample-lf.fasta")
LOGGER.shutdown()
try:
shutil.rmtree(DIRNAME)
except OSError:
pass
def test_creates_path():
"""creates a log path"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = os.path.join(DIRNAME, LOGFILE_NAME)
LOGGER.input_file("sample.fasta")
LOGGER.shutdown()
assert os.path.exists(DIRNAME)
assert os.path.exists(os.path.join(DIRNAME, LOGFILE_NAME))
try:
shutil.rmtree(DIRNAME)
except OSError:
pass
def test_creates_path():
"""creates a log path"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = LOGFILE_NAME
LOGGER.input_file(TEST_ROOTDIR / "sample-lf.fasta")
LOGGER.shutdown()
assert DIRNAME.exists()
assert LOGFILE_NAME.exists()
try:
shutil.rmtree(DIRNAME)
except OSError:
pass
def test_tracks_args():
"""details on host, python version should be present in log"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = os.path.join(LOGFILE_NAME)
LOGGER.input_file("sample.fasta")
LOGGER.shutdown()
with open(LOGFILE_NAME, "r") as infile:
contents = "".join(infile.readlines())
for label in ["system_details", "python", "user", "command_string"]:
assert contents.count(label) == 1, (label, contents.count(label))
try:
os.remove(LOGFILE_NAME)
except OSError:
pass
def test_caching():
"""should cache calls prior to logging"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.input_file(TEST_ROOTDIR / "sample-lf.fasta")
assert ("sample-lf.fasta" in LOGGER._messages[-2]
and "md5sum" in LOGGER._messages[-1])
LOGGER.log_versions(["numpy"])
assert "numpy==" in LOGGER._messages[-1]
LOGGER.log_file_path = LOGFILE_NAME
LOGGER.shutdown()
try:
shutil.rmtree(DIRNAME)
except OSError:
pass
def test_tracks_args():
"""details on host, python version should be present in log"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = LOGFILE_NAME
LOGGER.input_file(TEST_ROOTDIR / "sample-lf.fasta")
LOGGER.shutdown()
contents = LOGFILE_NAME.read_text()
for label in ["system_details", "python", "user", "command_string"]:
assert contents.count(f"\t{label}") == 1, (
label,
contents.count(label),
)
try:
shutil.rmtree(DIRNAME)
except OSError:
pass
def test_tracks_versions_module():
"""should track version if package is a module"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = os.path.join(LOGFILE_NAME)
import numpy
expect = "numpy==%s" % numpy.__version__
LOGGER.log_versions(numpy)
LOGGER.shutdown()
del numpy
with open(LOGFILE_NAME, "r") as infile:
contents = "".join(infile.readlines())
for line in contents.splitlines():
if "version :" in line and "numpy" in line:
assert expect in line, line
try:
os.remove(LOGFILE_NAME)
except OSError:
pass
def test_logging_text():
"""correctly logs text data"""
text = "abcde\nedfgu\nyhbnd"
hexd = "f06597f8a983dfc93744192b505a8af9"
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = LOGFILE_NAME
LOGGER.text_data(text, label="UNIQUE")
LOGGER.shutdown()
contents = LOGFILE_NAME.read_text().splitlines()
unique = None
for line in contents:
if "UNIQUE" in line:
unique = line
break
assert hexd in unique
try:
shutil.rmtree(DIRNAME)
except OSError:
pass
def test_mdsum_input():
"""md5 sum of input file should be correct"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = os.path.join(LOGFILE_NAME)
LOGGER.input_file("sample.fasta")
LOGGER.shutdown()
with open(LOGFILE_NAME, "r") as infile:
num = 0
for line in infile:
line = line.strip()
if "input_file_path md5sum" in line:
assert "96eb2c2632bae19eb65ea9224aaafdad" in line
num += 1
assert num == 1
try:
os.remove(LOGFILE_NAME)
except OSError:
pass
def test_tracks_versions_string():
"""should track version if package name is a string"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = LOGFILE_NAME
LOGGER.log_versions("numpy")
LOGGER.shutdown()
import numpy
expect = "numpy==%s" % numpy.__version__
del numpy
with open(LOGFILE_NAME, "r") as infile:
contents = "".join(infile.readlines())
for line in contents.splitlines():
if "version :" in line and "numpy" in line:
assert expect in line, line
try:
shutil.rmtree(DIRNAME)
except OSError:
pass
def test_tracks_versions_empty():
"""should track version of scitrack"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = LOGFILE_NAME
LOGGER.input_file(TEST_ROOTDIR / "sample-lf.fasta")
LOGGER.log_versions()
LOGGER.shutdown()
contents = LOGFILE_NAME.read_text()
for label in ["system_details", "python", "user", "command_string"]:
assert contents.count(f"\t{label}") == 1, (
label,
contents.count(label),
)
for line in contents.splitlines():
if "version :" in line:
assert "==%s" % __version__ in line, line
try:
shutil.rmtree(DIRNAME)
except OSError:
pass
def test_tracks_versions():
"""should track versions"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = os.path.join(LOGFILE_NAME)
LOGGER.input_file("sample.fasta")
LOGGER.log_versions(["numpy"])
LOGGER.shutdown()
with open(LOGFILE_NAME, "r") as infile:
contents = "".join(infile.readlines())
for label in ["system_details", "python", "user", "command_string"]:
assert contents.count(label) == 1, (label, contents.count(label))
for line in contents.splitlines():
if "version :" in line:
if "numpy" not in line:
assert "==%s" % __version__ in line, line
else:
assert "numpy" in line, line
print("\n\n", contents)
try:
os.remove(LOGFILE_NAME)
except OSError:
pass
def test_tracks_locals():
"""details on local arguments should be present in log"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = os.path.join(LOGFILE_NAME)
def track_func(a=1, b="abc"):
LOGGER.log_args()
track_func()
LOGGER.shutdown()
with open(LOGFILE_NAME, "r") as infile:
for line in infile:
index = line.find("params :")
if index > 0:
got = eval(line.split("params :")[1])
break
assert got == dict(a=1, b="abc")
try:
os.remove(LOGFILE_NAME)
pass
except OSError:
pass
