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_subset_of__rejects_dictionary():
spec = ValuesIntersect("abc")
assert_raises(MakefileError, spec, _DUMMY_PATH, {"a": 1, "b": 2})
def test_intersects__default_set__valid_value():
spec = ValuesIntersect(range(5), default=[3, 4])
assert_equal(spec.default, [3, 4])
def test_intersects__default_not_set():
spec = ValuesIntersect(range(5))
assert_is(spec.default, DEFAULT_NOT_SET)
def test_intersects__chars__case_sensitive__rejects_differences_in_case():
spec = ValuesIntersect("abcdefghijkl")
assert_raises(MakefileError, spec, _DUMMY_PATH, "A BIG DEAL")
def test_intersects__chars__case_sensitive():
spec = ValuesIntersect("abcdefghijkl")
spec(_DUMMY_PATH, "a big deal")
def test_intersects__case_sensitive__value_in_not_set():
spec = ValuesIntersect(("Abc", "bCe", "cdE"))
assert_raises(MakefileError, spec, _DUMMY_PATH, ["Bce"])
def test_intersects__case_sensitive__value_in_set():
spec = ValuesIntersect(("Abc", "bCe", "cdE"))
spec(_DUMMY_PATH, ["bCe"])
def test_intersects__empty_set():
spec = ValuesIntersect(range(5))
assert_raises(MakefileError, spec, _DUMMY_PATH, [])
def test_intersects__some_values_in_set():
spec = ValuesIntersect(range(5))
spec(_DUMMY_PATH, [4, 5])
def test_intersects__single_value_not_in_set():
spec = ValuesIntersect(range(5))
assert_raises(MakefileError, spec, _DUMMY_PATH, [5])
def test_intersects__multiple_values_in_set():
spec = ValuesIntersect(range(5))
spec(_DUMMY_PATH, [1, 4])
def test_intersects__single_value_in_set():
spec = ValuesIntersect(range(5))
spec(_DUMMY_PATH, [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(), 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"))
_VALIDATION_OPTIONS = {
# Sequencing platform, used to tag read-groups.
"Platform":
StringIn(("CAPILLARY", "LS454", "ILLUMINA", "SOLID", "HELICOS",
"IONTORRENT", "PACBIO"),
default="ILLUMINA"),
# Offset for quality scores in FASTQ files.
"QualityOffset":