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_value_ge__default_set__valid_value():
spec = ValueGE(10, default=10)
assert_equal(spec.default, 10)
def test_is_value_ge__default_not_set():
spec = ValueGE(10)
assert_is(spec.default, DEFAULT_NOT_SET)
def test_value_ge__custom_description():
spec = ValueGE('Bar', description='no less than {rvalue}')
assert_equal(spec.description, "no less than 'Bar'")
def test_value_ge__default_description():
spec = ValueGE('Foo')
assert_equal(spec.description, "value >= 'Foo'")
def test_value_ge__accepts_value_gt__with_key():
spec = ValueGE(7, key=len)
spec(_DUMMY_PATH, "abcdefgh")
def test_value_ge__accepts_value_lt__with_key():
spec = ValueGE(7, key=len)
assert_raises(MakefileError, spec, _DUMMY_PATH, "abcdef")
def test_value_ge__accepts_value_gt():
spec = ValueGE(7)
spec(_DUMMY_PATH, 8)
def test_value_ge__rejects_value_lt():
spec = ValueGE(7)
assert_raises(MakefileError, spec, _DUMMY_PATH, 6)
# 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":
ValueIn((33, 64, "Solexa"), default=33),
# Split a lane into multiple entries, one for each (pair of) file(s)
"SplitLanesByFilenames":
Or(IsBoolean, IsListOf(IsStr), default=True),
# Format to use when compressing FASTQ files ("gz" or "bz2")
"CompressionFormat":