def test_specs__path_is_displayed_in_exception():
def _path_is_displayed_in_exception(spec, value):
assert_raises_regexp(MakefileError, _DUMMY_PATH_STR, spec, _DUMMY_PATH,
value)
yield _path_is_displayed_in_exception, IsInt(), "foo"
yield _path_is_displayed_in_exception, IsUnsignedInt(), -1
yield _path_is_displayed_in_exception, IsFloat(), "abc"
yield _path_is_displayed_in_exception, IsBoolean(), 1
yield _path_is_displayed_in_exception, IsStr(), 1
yield _path_is_displayed_in_exception, IsNone(), 1
yield _path_is_displayed_in_exception, ValueLT(0), 1
yield _path_is_displayed_in_exception, ValueLE(0), 1
yield _path_is_displayed_in_exception, ValueGE(0), -1
yield _path_is_displayed_in_exception, ValueGT(0), -1
yield _path_is_displayed_in_exception, ValueIn([1]), 2
yield _path_is_displayed_in_exception, ValuesIntersect([1]), [2]
yield _path_is_displayed_in_exception, ValuesSubsetOf([1]), [2]
yield _path_is_displayed_in_exception, ValueMissing(), True
yield _path_is_displayed_in_exception, And(IsStr), 1
yield _path_is_displayed_in_exception, Or(IsStr), 1
yield _path_is_displayed_in_exception, Xor(IsStr, IsInt), True
yield _path_is_displayed_in_exception, Not(IsInt), 1
yield _path_is_displayed_in_exception, StringIn("abc"), 1
yield _path_is_displayed_in_exception, StringsIntersect("abc"), [1]
yield _path_is_displayed_in_exception, StringsSubsetOf("abc"), [1]
yield _path_is_displayed_in_exception, StringIsUppercase(), 1
yield _path_is_displayed_in_exception, StringStartsWith("FOO"), 1
yield _path_is_displayed_in_exception, StringEndsWith("FOO"), 1
yield _path_is_displayed_in_exception, IsListOf(IsInt), "foo"
yield _path_is_displayed_in_exception, IsDictOf(IsInt, IsInt), 1
def test_is_float__default_set__valid_value():
spec = IsFloat(default=3.14)
assert_equal(spec.default, 3.14)
def test_is_float__default_not_set():
spec = IsFloat()
assert_is(spec.default, DEFAULT_NOT_SET)
def test_is_float__custom_description():
custom_desc = "a floaty, float"
spec = IsFloat(description=custom_desc)
assert_equal(spec.description, custom_desc)
def test_is_float__default_description():
spec = IsFloat()
assert_equal(spec.description, "a float")
def _reject_not_str(value):
spec = IsFloat()
assert_raises(MakefileError, spec, _DUMMY_PATH, value)
def test_is_float__accepts_float():
spec = IsFloat()
spec(_DUMMY_PATH, 1.0)
_VALID_BED_NAME = _VALID_TARGET_NAME = \
And(_alphanum_check(whitelist=".-"),
ValueGE(2, key=len, description="at least two characters long"))
_VALIDATION_OPTIONS = {
"BamPath": IsStr,
"--MinMappingQuality": IsUnsignedInt(default=25),
"--MinAlignmentLength": IsUnsignedInt(default=25),
"--NoReadsChecked": IsUnsignedInt(default=5000)
}
_VALIDATION_GCCORRECT = {
"Enabled": IsBoolean(default=False),
"--NoRegions": Or(IsUnsignedInt, IsStr, default=200),
"--ChromUsed": Or(IsStr, IsUnsignedInt, default="all"), ## the is new
"--MappaUniqueness": IsFloat(default=0.9)
}
_VALIDATION_NUCLEO = {
"Enabled": IsBoolean(default=False),
"Apply_GC_Correction": IsBoolean(default=True),
"ExcludeBed": EXCLUDEBED,
"--NucleosomeFlanks": IsUnsignedInt(default=25),
"--NucleosomeSize": IsUnsignedInt(default=147),
"--NucleosomeOffset": IsUnsignedInt(default=12)
}
_VALIDATION_METHYL = {
"Enabled": IsBoolean(default=False),
"ExcludeBed": EXCLUDEBED,
"--ReadBases": IsUnsignedInt(default=15),
"--MinBaseQuality": IsUnsignedInt(default=20),