def test_and__default_not_set():
spec = And(IsInt, ValueIn(list(range(10))))
assert spec.default is DEFAULT_NOT_SET
def test_value_in__single_value_in_set():
spec = ValueIn(list(range(5)))
spec(_DUMMY_PATH, 1)
def test_and__rejects_when_both_is_false():
spec = And(IsFloat, ValueIn((0.0, 1, 2)))
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, 3)
def test_or__defaults_not_set_in_specs():
with pytest.raises(ValueError):
Or(IsInt(default=10), ValueIn((10, )))
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"),
}
}
},
def test_and__defaults_not_set_in_specs():
with pytest.raises(ValueError):
And(IsInt(default=10), ValueIn((list(range(100)))))
def test_or__default_set__valid_value():
spec = Or(IsInt, ValueIn((10, )), default=17)
assert spec.default == 17
def test_value_in__default_description():
spec = ValueIn(("Abc", "bCe", "cdE"))
assert spec.description == "value in 'Abc', 'bCe', or 'cdE'"
def test_value_in__custom_description():
spec = ValueIn(("Abc", "bCe", "cdE"), description="One of {rvalue}")
assert spec.description == "One of 'Abc', 'bCe', or 'cdE'"
def test_value_in__case_sensitive__value_in_set():
spec = ValueIn(("Abc", "bCe", "cdE"))
spec(_DUMMY_PATH, "bCe")
def test_value_in__case_sensitive__value_in_not_set():
spec = ValueIn(("Abc", "bCe", "cdE"))
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, "Bce")
def test_value_in__single_value_not_in_set__with_key():
spec = ValueIn(list(range(5)), key=len)
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, "abcde")
def test_value_in__single_value_in_set__with_key():
spec = ValueIn(list(range(5)), key=len)
spec(_DUMMY_PATH, "a")
def test_value_in__single_value_not_in_set():
spec = ValueIn(list(range(5)))
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, 5)
def test_and__default_set__valid_value():
spec = And(IsInt, ValueIn(list(range(30))), default=20)
assert spec.default == 20
def test_is_value_in__default_not_set():
spec = ValueIn(list(range(5)))
assert spec.default is DEFAULT_NOT_SET
def test_and__default_set__must_meet_spec():
with pytest.raises(ValueError):
And(IsInt, ValueIn((1, )), default=5)
def test_is_value_in__default_set__valid_value():
spec = ValueIn(list(range(5)), default=4)
assert spec.default == 4
def test_or__default_not_set():
spec = Or(IsInt, ValueIn((10, )))
assert spec.default is DEFAULT_NOT_SET
def test_is_value_in__default_set__must_meet_spec():
with pytest.raises(ValueError):
ValueIn(list(range(5)), default=5)
def test_or__default_set__must_meet_spec():
with pytest.raises(ValueError):
Or(IsInt, ValueIn((10, )), default=5.5)
def test_is_value_in__handles_types(value):
spec = ValueIn((1, 2, 3, 4))
with pytest.raises(MakefileError,
match="Expected value: value in 1, 2, 3, or 4"):
spec(_DUMMY_PATH, value)
"CollapsedTruncated": IsBoolean(default=False),
"Paired": IsBoolean(default=False),
"Singleton": IsBoolean(default=False),
}
_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":
RemovedOption(),
"CompressionFormat":
RemovedOption(),
"AdapterRemoval": {
"Version": RemovedOption(),
"--pcr1": IsStr,
"--pcr2": IsStr,
"--adapter1": IsStr,
"--adapter2": IsStr,
"--adapter-list": IsStr,
"--maxns": IsUnsignedInt,
"--minquality": IsUnsignedInt,
"--trimns": Or(IsNone, IsBoolean),
def test_and__accepts_when_all_true():
spec = And(IsFloat, ValueIn((0.0, 1, 2)))
spec(_DUMMY_PATH, 0.0)
# change the behavior of old makefiles.
for key in _READ_TYPES:
result.setdefault(key, False)
return result, _VALID_EXCLUDE_DICT
_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,
"--adapter-list": IsStr,
"--maxns": IsUnsignedInt,
"--minquality": IsUnsignedInt,
with pytest.raises(ValueError):
IsDictOf(IsInt, IsInt(default=10))
###############################################################################
###############################################################################
# Path is displayed in exception
_PATH_IN_EXCEPTION_VALUES = (
(IsInt(), "foo"),
(IsUnsignedInt(), -1),
(IsFloat(), "abc"),
(IsBoolean(), 1),
(IsStr(), 1),
(IsNone(), 1),
(ValueIn([1]), 2),
(ValuesIntersect([1]), [2]),
(ValuesSubsetOf([1]), [2]),
(ValueMissing(), True),
(And(IsStr), 1),
(Or(IsStr), 1),
(Not(IsInt), 1),
(StringIn("abc"), 1),
(StringStartsWith("FOO"), 1),
(StringEndsWith("FOO"), 1),
(IsListOf(IsInt), "foo"),
(IsDictOf(IsInt, IsInt), 1),
)
@pytest.mark.parametrize("spec, value", _PATH_IN_EXCEPTION_VALUES)