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 _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_subset_of__default_set__valid_value():
spec = ValuesSubsetOf(range(5), default=[3, 4])
assert_equal(spec.default, [3, 4])
def test_subset_of__default_not_set():
spec = ValuesSubsetOf(range(5))
assert_is(spec.default, DEFAULT_NOT_SET)
def test_subset_of__chars__case_sensitive__rejects_differences_in_case():
spec = ValuesSubsetOf("abcdefghijkl ")
assert_raises(MakefileError, spec, _DUMMY_PATH, "A big DEAL")
def test_subset_of__chars__case_sensitive():
spec = ValuesSubsetOf("abcdefghijkl ")
spec(_DUMMY_PATH, "a big deal")
def test_subset_of__case_sensitive__value_in_not_set():
spec = ValuesSubsetOf(("Abc", "bCe", "cdE"))
assert_raises(MakefileError, spec, _DUMMY_PATH, ["Bce"])
def test_subset_of__case_sensitive__value_in_set():
spec = ValuesSubsetOf(("Abc", "bCe", "cdE"))
spec(_DUMMY_PATH, ["bCe"])
def test_subset_of__empty_set():
spec = ValuesSubsetOf(range(5))
spec(_DUMMY_PATH, [])
def test_subset_of__multiple_values_not_in_set():
spec = ValuesSubsetOf(range(5))
assert_raises(MakefileError, spec, _DUMMY_PATH, [4, 5])
def test_subset_of__multiple_values_in_set():
spec = ValuesSubsetOf(range(5))
spec(_DUMMY_PATH, [1, 4])
def test_subset_of__single_value_in_set():
spec = ValuesSubsetOf(range(5))
spec(_DUMMY_PATH, [1])
"PhylogeneticInference": {
IsStr: {
# Which program to use; TODO: Add support for other programs
"Program": StringIn(("examl", ), default="examl"),
# Exclude one or more samples from the phylogeny
"ExcludeSamples": [IsStr],
# Which samples to root the final trees on / or midpoint rooting
"RootTreesOn": [IsStr],
# Create a tree per gene, for each region of interest,
# or create a supermatrix tree from all regions specified.
"PerGeneTrees": IsBoolean(default=False),
# Selection of regions of interest / settings per region
"RegionsOfInterest": {
IsStr: {
"Partitions":
Or(And(IsStr, ValuesSubsetOf("123456789X")),
ValueIn([False]),
default=REQUIRED_VALUE),
"SubsetRegions":
Or(IsStr, IsNone, default=None),
},
},
"SubsetRegions": {
IsStr: IsStr,
},
"ExaML": {
"Bootstraps": IsUnsignedInt(default=100),
"Replicates": IsUnsignedInt(default=1),
"Model": StringIn(("GAMMA", "PSR"), default="gamma"),
}
}
"--adjust": IsUnsignedInt,
"--iter": IsUnsignedInt,
"--forward": IsNone,
"--reverse": IsNone,
"--var-disp": IsNone,
"--jukes-cantor": IsNone,
"--diff-hangs": IsNone,
"--fix-nicks": IsNone,
"--use-raw-nick-freq": IsNone,
"--single-stranded": IsNone,
"--seq-length": IsUnsignedInt,
},
# Exclude READ_TYPES from alignment/analysis
"ExcludeReads":
Or(IsNone, ValuesSubsetOf(_READ_TYPES), default=[]),
# Features of pipeline
"Features":
Or(IsNone,
ValuesSubsetOf(("Raw BAM", "Realigned BAM", "Coverage", "Summary",
"mapDamage", "Depths", "DuplicateHist")),
default=["Realigned BAM", "Coverage", "Summary", "mapDamage",
"Depths"]),
}
_VALIDATION = {
"Options": _VALIDATION_OPTIONS,
"Prefixes": {