def test_import_usda(usda_data_dir):
'''
Sample one food is correctly imported from USDA
Meaning there should be: description, protein factor, fat factor,
carbohydrate factor and a {internal_nutrient_name} column for each nutrient
hardcoded in _mapping.
'''
foods = foods_.import_usda(usda_data_dir)
expected = dedent('''\
description Butter, salted
Conversion factor: protein 4270
Conversion factor: fat 8790
Conversion factor: carbohydrate 3870
alpha linolenic acid 0.00315
caffeine 0
calcium 0.00024
carbohydrate 0.0006
carotenoids 1.58e-06
cholesterol 0.00215
choline 0.000188
copper 0
energy 7170
fat 0.8111
fatty acids 0.54646
fiber 0
fluoride 2.8e-08
folate 3e-08
folate, added 0
iron 2e-07
linoleic acid 0.02728
linoleic acid + alpha linolenic acid 0.03043
magnesium 2e-05
manganese 0
mass 1
niacin 4.2e-07
pantothenic acid 1.1e-06
phosphorus 0.00024
potassium 0.00024
protein 0.0085
riboflavin 3.4e-07
selenium 1e-08
sodium 0.00643
sugars, added 0.0006
thiamin 5e-08
vitamin a 6.84e-06
vitamin a, preformed 6.71e-06
vitamin b12 1.7e-09
vitamin b6 3e-08
vitamin c 0
vitamin d 0
vitamin e 2.32e-05
vitamin e, added 0
vitamin k 7e-08
water 0.1587
zinc 9e-07'''
)
assert_text_equals(foods.loc[1001].to_string(), expected)
def test_configure(temp_dir_cwd, capsys, caplog):
log_file = Path('file.log')
stderr_handler, file_handler = logging_.configure(log_file)
assert isinstance(stderr_handler, logging.StreamHandler)
assert isinstance(file_handler, logging.FileHandler)
logger = logging.getLogger(__name__)
logger.info('Fake info')
logger.debug('Ignored debug')
logger.setLevel(logging.DEBUG)
logger.debug('Fake debug')
# stderr
#
# - level is INFO
# - terse format
expected = 'I: Fake info\n'
actual = capsys.readouterr()[1]
assert_text_equals(actual, expected)
# log file
#
# - level is DEBUG
# - long format with fairly unambiguous source
log_file_content = path_.read(log_file)
def prefix(log_type, package, module_name):
return r'{} [0-9]{{4}}-[0-9]{{2}}-[0-9]{{2}} [0-9]{{2}}:[0-9]{{2}}:[0-9]{{2}},[0-9]{{3}} {} \({}:[0-9]+\):'.format(
log_type, package, module_name
)
pattern = dedent('''\
{}
Fake info
{}
Fake debug
'''
.format(
prefix('I', __name__, 'test_logging'),
prefix('D', __name__, 'test_logging'),
)
)
assert re.match(pattern, log_file_content, re.MULTILINE), 'Actual:{}\n\nExpected to match:\n{}'.format(log_file_content, pattern)
def assert_equals(file1, file2, contents=True, name=True, mode=True):
'''
Assert 2 files are equal
Parameters
-----------
file1 : Path
file2 : Path
contents : bool
Assert file contents are equal
name : bool
Assert file names are equal
mode : bool
Assert the last 3 octal digits of file modes are equal
'''
if name:
assert file1.name == file2.name
if contents:
assert_text_equals(read(file1), read(file2))
if mode:
assert file1.stat().st_mode == file2.stat().st_mode