def test_is_str__rejects_empty_str():
with pytest.raises(MakefileError):
IsStr()(_DUMMY_PATH, "")
with pytest.raises(MakefileError):
IsStr(min_len=1)(_DUMMY_PATH, "")
with pytest.raises(MakefileError):
IsStr(min_len=2)(_DUMMY_PATH, "")
with pytest.raises(MakefileError):
IsStr(min_len=3)(_DUMMY_PATH, "")
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))
def test_is_str__min_len_2():
spec = IsStr(min_len=2)
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, "")
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, "a")
spec(_DUMMY_PATH, "ab")
spec(_DUMMY_PATH, "abc")
% (", ".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
# Genotyping settings; note that explicit lists must not be used here, to allow
# proper inheritance of default values. Use IsListOf instead.
_VALIDATION_GENOTYPES = {
"Padding": IsUnsignedInt,
"GenotypeEntirePrefix": IsBoolean(default=False),
"MPileup": {
StringStartsWith("-"): Or(IsInt, IsStr, IsNone),
},
"BCFTools": {
StringStartsWith("-"): Or(IsInt, IsStr, IsNone),
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(),
"RealignedBAM": RemovedOption(),
"Summary": IsBoolean(default=True),
"mapDamage": StringIn(("rescale", "model", "plot")),
}
def test_is_str__min_len_0():
spec = IsStr(min_len=0)
spec(_DUMMY_PATH, "")
spec(_DUMMY_PATH, "a")
spec(_DUMMY_PATH, "ab")
def test_is_str__default_set__must_meet_spec():
with pytest.raises(ValueError):
IsStr(default=17)
def test_is_str__default_set__valid_value():
spec = IsStr(default="abc")
assert spec.default == "abc"
def test_is_dict_of__defaults_not_set_in_value_specs():
with pytest.raises(ValueError):
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),
)
def test_is_str__custom_description():
custom_desc = "a ball of string"
spec = IsStr(description=custom_desc)
assert spec.description == custom_desc
def test_is_str__default_description():
spec = IsStr()
assert spec.description == "a non-empty string"
def test_is_str__rejects_not_str(value):
spec = IsStr()
with pytest.raises(MakefileError,
match="Expected value: a non-empty string"):
spec(_DUMMY_PATH, value)
def test_is_str__rejects_negative_min_len():
with pytest.raises(ValueError):
IsStr(min_len=-1)
def test_is_str__accepts_empty_str():
spec = IsStr(min_len=0)
spec(_DUMMY_PATH, "")
def test_is_str__accepts_standard_str():
spec = IsStr()
spec(_DUMMY_PATH, "abc")
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":
def test_is_str__default_not_set():
spec = IsStr()
assert spec.default is DEFAULT_NOT_SET
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": RemovedOption(),
"SpeciesName": RemovedOption(),
"CommonName": RemovedOption(),
"Sex": IsStr(),
"Gender": RemovedOption(),
}
}
_VALIDATION_SAMPLES[_VALIDATION_SUBSAMPLE_KEY] = _VALIDATION_SAMPLES
# Genotyping settings; note that explicit lists must not be used here, to allow
# proper inheritance of default values. Use IsListOf instead.
_VALIDATION_GENOTYPES = {
"Padding": IsUnsignedInt,
"GenotypeEntirePrefix": IsBoolean(default=False),
"MPileup": {
StringStartsWith("-"): Or(IsInt, IsStr, IsNone)
},
"BCFTools": {
StringStartsWith("-"): Or(IsInt, IsStr, IsNone)