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_in__default_set__valid_value():
spec = ValueIn(range(5), default=4)
assert_equal(spec.default, 4)
def test_is_value_in__default_not_set():
spec = ValueIn(range(5))
assert_is(spec.default, DEFAULT_NOT_SET)
def test_value_in__custom_description():
spec = ValueIn(("Abc", "bCe", "cdE"), description="One of {rvalue}")
assert_equal(spec.description, "One of 'Abc', 'bCe', or 'cdE'")
def test_value_in__default_description():
spec = ValueIn(("Abc", "bCe", "cdE"))
assert_equal(spec.description, "value in 'Abc', 'bCe', or 'cdE'")
def test_value_in__case_sensitive__value_in_not_set():
spec = ValueIn(("Abc", "bCe", "cdE"))
assert_raises(MakefileError, spec, _DUMMY_PATH, "Bce")
def test_value_in__case_sensitive__value_in_set():
spec = ValueIn(("Abc", "bCe", "cdE"))
spec(_DUMMY_PATH, "bCe")
def test_value_in__single_value_not_in_set__with_key():
spec = ValueIn(range(5), key=len)
assert_raises(MakefileError, spec, _DUMMY_PATH, "abcde")
def test_value_in__single_value_in_set__with_key():
spec = ValueIn(range(5), key=len)
spec(_DUMMY_PATH, "a")
def test_value_in__single_value_not_in_set():
spec = ValueIn(range(5))
assert_raises(MakefileError, spec, _DUMMY_PATH, 5)
def test_value_in__single_value_in_set():
spec = ValueIn(range(5))
spec(_DUMMY_PATH, 1)
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"),
}
}
},
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":
ValueIn(("gz", "bz2"), default="bz2"),
"AdapterRemoval": {
"Version": ValueIn(("v1.4", "v1.5+"), default="v1.5+"),
"--pcr1": IsStr,
"--pcr2": IsStr,
"--adapter1": IsStr,
"--adapter2": IsStr,
"--maxns": IsUnsignedInt,
"--minquality": IsUnsignedInt,
"--trimns": Or(IsNone, IsBoolean),