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import contextlib
import sys
from collections import Counter
from pathlib import Path
import pytest
from scitrack import (
CachingLogger,
get_file_hexdigest,
get_package_name,
get_text_hexdigest,
get_version_for_package,
)
__version__ = "2024.10.8"
TEST_ROOTDIR = Path(__file__).parent
DIRNAME = "delme"
LOGFILE_NAME = "delme.log"
@pytest.fixture
def logfile(tmp_path):
return tmp_path / LOGFILE_NAME
def test_creates_path(logfile):
"""creates a log path"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = logfile
LOGGER.input_file(TEST_ROOTDIR / "sample-lf.fasta")
LOGGER.shutdown()
assert logfile.exists()
def test_set_path_if_exists(logfile):
"""cannot change an existing logging path"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = logfile
LOGGER.input_file(TEST_ROOTDIR / "sample-lf.fasta")
with pytest.raises(AttributeError):
LOGGER.log_file_path = logfile.parent / "invalid.log"
LOGGER.shutdown()
def test_tracks_args(logfile):
"""details on host, python version should be present in log"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = logfile
LOGGER.input_file(TEST_ROOTDIR / "sample-lf.fasta")
LOGGER.shutdown()
contents = logfile.read_text()
for label in ["system_details", "python", "user", "command_string"]:
assert contents.count(f"\t{label}") == 1, (
label,
contents.count(label),
)
def test_tracks_locals(logfile):
"""details on local arguments should be present in log"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = logfile
def track_func(a=1, b="abc"):
LOGGER.log_args()
track_func()
LOGGER.shutdown()
log_data = logfile.read_text().splitlines()
for line in log_data:
index = line.find("params :")
if index > 0:
got = eval(line.split("params :")[1])
break
assert got == dict(a=1, b="abc")
def test_tracks_locals_skip_module(logfile):
"""local arguments should exclude modules"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = logfile
def track_func(a=1, b="abc"):
import gzip # noqa
LOGGER.log_args()
track_func()
LOGGER.shutdown()
for line in logfile.read_text().splitlines():
index = line.find("params :")
if index > 0:
got = eval(line.split("params :")[1])
break
assert got == dict(a=1, b="abc")
def test_package_inference():
"""correctly identify the package name"""
name = get_package_name(CachingLogger)
assert name == "scitrack"
def test_package_versioning():
"""correctly identify versions for specified packages"""
vn = get_version_for_package("numpy")
assert type(vn) is str
with contextlib.suppress(ValueError):
get_version_for_package("gobbledygook")
with contextlib.suppress(ValueError):
get_version_for_package(1)
def test_tracks_versions(logfile):
"""should track versions"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = logfile
LOGGER.input_file(TEST_ROOTDIR / "sample-lf.fasta")
LOGGER.log_versions(["numpy"])
LOGGER.shutdown()
contents = logfile.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:
if "numpy" not in line:
assert f"=={__version__}" in line, line
else:
assert "numpy" in line, line
def test_caching(logfile):
"""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
LOGGER.shutdown()
def test_shutdown(logfile):
"""correctly purges contents"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = logfile
LOGGER.input_file(TEST_ROOTDIR / "sample-lf.fasta")
LOGGER.shutdown()
def test_tracks_versions_empty(logfile):
"""should track version of scitrack"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = logfile
LOGGER.input_file(TEST_ROOTDIR / "sample-lf.fasta")
LOGGER.log_versions()
LOGGER.shutdown()
contents = logfile.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 f"=={__version__}" in line, line
def test_tracks_versions_string(logfile):
"""should track version if package name is a string"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = logfile
LOGGER.log_versions("numpy")
LOGGER.shutdown()
import numpy
expect = f"numpy=={numpy.__version__}"
del numpy
for line in logfile.read_text().splitlines():
if "version :" in line and "numpy" in line:
assert expect in line, line
def test_get_version_for_package():
"""should track version if package is a module"""
import numpy
got = get_version_for_package(numpy)
assert got == numpy.__version__
# one with a callable
pyfile = TEST_ROOTDIR / "delme.py"
pyfile.write_text("\n".join(["def version():", " return 'my-version'"]))
sys.path.append(TEST_ROOTDIR)
import delme
got = get_version_for_package("delme")
assert got == "my-version"
pyfile.unlink()
# func returns a list
pyfile.write_text("version = ['my-version']\n")
from importlib import reload
got = get_version_for_package(reload(delme))
assert got == "my-version"
pyfile.unlink()
def test_tracks_versions_module(logfile):
"""should track version if package is a module"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = logfile
import numpy
expect = f"numpy=={numpy.__version__}"
LOGGER.log_versions(numpy)
LOGGER.shutdown()
del numpy
for line in logfile.read_text().splitlines():
if "version :" in line and "numpy" in line:
assert expect in line, line
def test_appending(logfile):
"""appending to an existing logfile should work"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = logfile
LOGGER.input_file(TEST_ROOTDIR / "sample-lf.fasta")
LOGGER.shutdown()
records = Counter()
for line in logfile.read_text().splitlines():
records[line] += 1
vals = set(list(records.values()))
assert vals == {1}
LOGGER = CachingLogger(create_dir=True)
LOGGER.mode = "a"
LOGGER.log_file_path = logfile
LOGGER.input_file(TEST_ROOTDIR / "sample-lf.fasta")
LOGGER.shutdown()
records = Counter()
for line in logfile.read_text().splitlines():
records[line] += 1
vals = set(list(records.values()))
assert vals == {2}
def test_mdsum_input(logfile):
"""md5 sum of input file should be correct"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = logfile
# first file has LF, second has CRLF line endings
hex_path = [
("96eb2c2632bae19eb65ea9224aaafdad", "sample-lf.fasta"),
("e7e219f66be15d8afc7cdb85303305a7", "sample-crlf.fasta"),
]
LOGGER.input_file(TEST_ROOTDIR / "sample-lf.fasta")
LOGGER.input_file(TEST_ROOTDIR / "sample-crlf.fasta")
LOGGER.shutdown()
with open(logfile) as infile:
num = 0
for line in infile:
for h, p in hex_path:
if p in line:
assert "input_file" in line
line = next(infile)
assert h in line
num += 1
assert num == len(hex_path)
def test_mdsum_output(logfile):
"""md5 sum of output file should be correct"""
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = logfile
# 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) 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)
def test_logging_text(logfile):
"""correctly logs text data"""
text = "abcde\nedfgu\nyhbnd"
hexd = "f06597f8a983dfc93744192b505a8af9"
LOGGER = CachingLogger(create_dir=True)
LOGGER.log_file_path = logfile
LOGGER.text_data(text, label="UNIQUE")
LOGGER.shutdown()
contents = logfile.read_text().splitlines()
unique = next((line for line in contents if "UNIQUE" in line), None)
assert hexd in unique
def test_logfile_path(logfile):
"""correctly assigned"""
LOGGER = CachingLogger(create_dir=True, log_file_path=logfile)
assert LOGGER.log_file_path == str(logfile)
LOGGER.shutdown()
def test_md5sum_text():
"""md5 sum for text data should be computed"""
data = "åbcde"
s = get_text_hexdigest(data)
assert s
data = "abcde"
s = get_text_hexdigest(data)
assert s
# loading contents from files with diff line-endings and check
hex_path = [
("96eb2c2632bae19eb65ea9224aaafdad", "sample-lf.fasta"),
("e7e219f66be15d8afc7cdb85303305a7", "sample-crlf.fasta"),
]
for h, p in hex_path:
p = TEST_ROOTDIR / p
data = p.read_bytes()
got = get_text_hexdigest(data)
assert got == h, (p, repr(data))
def test_get_text_hexdigest_invalid():
"""raises TypeError when invalid data provided"""
with pytest.raises(TypeError):
get_text_hexdigest(None)
with pytest.raises(TypeError):
get_text_hexdigest([])
def test_read_from_written(tmp_path):
"""create files with different line endings dynamically"""
text = "abcdeENDedfguENDyhbnd"
for ex, lf in (
("f06597f8a983dfc93744192b505a8af9", "\n"),
("39db5cc2f7749f02e0c712a3ece12ffc", "\r\n"),
):
p = tmp_path / "test.txt"
data = text.replace("END", lf)
p.write_bytes(data.encode("utf-8"))
expect = get_text_hexdigest(data)
assert expect == ex, (expect, ex)
got = get_file_hexdigest(p)
assert got == expect, f"FAILED: {lf!r}, {(ex, got)}"
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