def test_intersects__handles_types(value):
spec = ValuesIntersect(list(range(5)))
with pytest.raises(
MakefileError,
match="Expected value: one or more of 0, 1, 2, 3, and 4"):
spec(_DUMMY_PATH, value)
def test_subset_of__rejects_dictionary():
spec = ValuesIntersect("abc")
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, {"a": 1, "b": 2})
def test_intersects__default_set__valid_value():
spec = ValuesIntersect(list(range(5)), default=[3, 4])
assert spec.default == [3, 4]
def test_intersects__default_set__must_meet_spec():
with pytest.raises(ValueError):
ValuesIntersect(list(range(5)), default=[5])
def test_intersects__chars__case_sensitive__rejects_differences_in_case():
spec = ValuesIntersect("abcdefghijkl")
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, "A BIG DEAL")
def test_intersects__default_not_set():
spec = ValuesIntersect(list(range(5)))
assert spec.default is DEFAULT_NOT_SET
def test_intersects__case_sensitive__value_in_not_set():
spec = ValuesIntersect(("Abc", "bCe", "cdE"))
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, ["Bce"])
def test_intersects__single_value_in_set():
spec = ValuesIntersect(list(range(5)))
spec(_DUMMY_PATH, [1])
def test_intersects__empty_set():
spec = ValuesIntersect(list(range(5)))
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, [])
def test_intersects__case_sensitive__value_in_set():
spec = ValuesIntersect(("Abc", "bCe", "cdE"))
spec(_DUMMY_PATH, ["bCe"])
def test_intersects__some_values_in_set():
spec = ValuesIntersect(list(range(5)))
spec(_DUMMY_PATH, [4, 5])
def test_intersects__single_value_not_in_set():
spec = ValuesIntersect(list(range(5)))
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, [5])
def test_intersects__multiple_values_in_set():
spec = ValuesIntersect(list(range(5)))
spec(_DUMMY_PATH, [1, 4])
whitelist += string.ascii_letters + string.digits
return And(IsStr(min_len=min_len),
ValuesSubsetOf(whitelist, description=description))
# Valid names for prefixes
_VALID_PREFIX_NAME = And(
_alphanum_check(whitelist="._-*"),
Not(StringIn(["Options"] + [(s + "Reads") for s in _READ_TYPES])),
)
# Valid paths for prefixes; avoids some problems with e.g. Bowtie2
_VALID_PREFIX_PATH = And(IsStr(),
Not(ValuesIntersect('\\:?"<>|() \t\n\v\f\r')),
default=REQUIRED_VALUE)
# Valid strings for targets / samples / libraries / lanes
_VALID_TARGET_NAME = _alphanum_check(whitelist="._-", min_len=2)
_VALID_FEATURES_DICT = {
"Coverage": IsBoolean(default=True),
"Depths": IsBoolean(default=True),
"DuplicateHist": RemovedOption(),
"RawBAM": RemovedOption(),
"RealignedBAM": RemovedOption(),
"Summary": IsBoolean(default=True),
"mapDamage": StringIn(("rescale", "model", "plot")),
}
def test_intersects__chars__case_sensitive():
spec = ValuesIntersect("abcdefghijkl")
spec(_DUMMY_PATH, "a big deal")
description = "characters a-z, A-Z, 0-9%s allowed"
description %= (", and %r" % whitelist, ) if whitelist else ""
whitelist += string.ascii_letters + string.digits
return And(IsStr(), ValuesSubsetOf(whitelist, description=description))
# Valid names for prefixes
_VALID_PREFIX_NAME = \
And(_alphanum_check(whitelist="._-*"),
Not(StringIn(["Options"] + [(s + "Reads") for s in _READ_TYPES])))
# Valid paths for prefixes; avoids some problems with e.g. Bowtie2
_VALID_PREFIX_PATH = \
And(IsStr(), Not(ValuesIntersect("\\:?\"<>|() \t\n\v\f\r")),
default=REQUIRED_VALUE)
# Valid strings for targets / samples / libraries / lanes
_VALID_TARGET_NAME = \
And(_alphanum_check(whitelist="._-"),
ValueGE(2, key=len, description="at least two characters long"))
_VALID_FEATURES_DICT = {
"Coverage":
IsBoolean(default=True),
"Depths":
IsBoolean(default=True),
"DuplicateHist":
IsBoolean(default=False),
"RawBAM":
IsDictOf(IsInt, IsInt(default=10))
###############################################################################
###############################################################################
# Path is displayed in exception
_PATH_IN_EXCEPTION_VALUES = (
(IsInt(), "foo"),
(IsUnsignedInt(), -1),
(IsFloat(), "abc"),
(IsBoolean(), 1),
(IsStr(), 1),
(IsNone(), 1),
(ValueIn([1]), 2),
(ValuesIntersect([1]), [2]),
(ValuesSubsetOf([1]), [2]),
(ValueMissing(), True),
(And(IsStr), 1),
(Or(IsStr), 1),
(Not(IsInt), 1),
(StringIn("abc"), 1),
(StringStartsWith("FOO"), 1),
(StringEndsWith("FOO"), 1),
(IsListOf(IsInt), "foo"),
(IsDictOf(IsInt, IsInt), 1),
)
@pytest.mark.parametrize("spec, value", _PATH_IN_EXCEPTION_VALUES)
def test_specs__path_is_displayed_in_exception(spec, value):