def _alphanum_check(whitelist):
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))
return _validate_makefiles(config, makefiles)
def _alphanum_check(whitelist):
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":
return _validate_makefiles(makefiles)
def _alphanum_check(whitelist, min_len=1):
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(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(),
msa = mkfile["MultipleSequenceAlignment"]
defaults = msa.pop("Defaults")
defaults.setdefault("Program", "MAFFT")
defaults["MAFFT"].setdefault("Algorithm", "MAFFT")
for key in mkfile["Project"]["Regions"]:
msa[key] = fill_dict(msa.get(key, {}), defaults)
unknown_regions = set(msa) - set(mkfile["Project"]["Regions"])
if unknown_regions:
raise MakefileError("Unknown Regions of Interest in Genotyping: %s" \
% (", ".join(unknown_regions),))
# Recursive definition of sample tree
_VALIDATION_SUBSAMPLE_KEY = And(StringStartsWith("<"),
StringEndsWith(">"))
_VALIDATION_SAMPLES_KEY = And(IsStr, Not(_VALIDATION_SUBSAMPLE_KEY))
_VALIDATION_SAMPLES = {
_VALIDATION_SAMPLES_KEY: {
"GenotypingMethod": StringIn(("reference sequence",
"random sampling",
"samtools"),
default="samtools"),
"SpeciesName": IsStr, # Not used; left for backwards compatibility
"CommonName": IsStr, # Not used; left for backwards compatibility
"Sex": IsStr(),
"Gender": IsStr(),
}
}
_VALIDATION_SAMPLES[_VALIDATION_SUBSAMPLE_KEY] = _VALIDATION_SAMPLES
def test_and__default_set__must_meet_spec():
with pytest.raises(ValueError):
And(IsInt, ValueIn((1, )), default=5)
def test_and__defaults_not_set_in_specs():
with pytest.raises(ValueError):
And(IsInt(default=10), ValueIn((list(range(100)))))
def test_and__default_not_set():
spec = And(IsInt, ValueIn(list(range(10))))
assert spec.default is DEFAULT_NOT_SET
def test_and__default_set__valid_value():
spec = And(IsInt, ValueIn(list(range(30))), default=20)
assert spec.default == 20
def test_and__rejects_non_spec_tests():
with pytest.raises(TypeError):
And(id)
def test_and__rejects_no_tests():
with pytest.raises(ValueError):
And()
def test_and__rejects_when_both_is_false():
spec = And(IsFloat, ValueIn((0.0, 1, 2)))
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, 3)
def test_and__accepts_when_all_true():
spec = And(IsFloat, ValueIn((0.0, 1, 2)))
spec(_DUMMY_PATH, 0.0)
###############################################################################
###############################################################################
# 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):
with pytest.raises(MakefileError, match=_DUMMY_PATH_STR):
spec(_DUMMY_PATH, value)