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_dict_of__default_not_set():
spec = IsDictOf(IsInt, IsInt)
assert_is(spec.default, DEFAULT_NOT_SET)
def test_is_dict_of__default_set__valid_value():
spec = IsDictOf(IsInt, IsInt, default={1: 2})
assert_equal(spec.default, {1: 2})
def test_is_dict_of__default_description():
spec = IsDictOf(IsInt, IsStr)
assert_equal(spec.description, "{(an integer) : (a non-empty string)}")
def test_is_dict_of__rejects_non_dict():
spec = IsDictOf(IsInt, IsStr)
assert_raises(MakefileError, spec, _DUMMY_PATH, [])
def test_is_dict_of__correct_key_and_wrong_value_rejected():
spec = IsDictOf(IsInt, IsStr)
assert_raises(MakefileError, spec, _DUMMY_PATH, {1: 1})
def test_is_dict_of__mixed_rejected():
spec = IsDictOf(IsInt, IsStr)
assert_raises(MakefileError, spec, _DUMMY_PATH, {1: 1, 2: "foo"})
def test_is_dict_of__correct_key_and_value_accepted():
spec = IsDictOf(IsInt, IsStr)
spec(_DUMMY_PATH, {1: "foo"})
def test_is_dict_of__empty_dict_always_ok():
spec = IsDictOf(IsInt, IsStr)
spec(_DUMMY_PATH, {})
# proper inheritance of default values. Use IsListOf instead.
_VALIDATION_GENOTYPES = {
"Padding": IsUnsignedInt,
"GenotypeEntirePrefix": IsBoolean(default=False),
"MPileup": {
StringStartsWith("-"): Or(IsInt, IsStr, IsNone),
},
"BCFTools": {
StringStartsWith("-"): Or(IsInt, IsStr, IsNone),
},
"Random": {
"--min-distance-to-indels": IsUnsignedInt,
},
"VCF_Filter": {
"MaxReadDepth":
Or(IsUnsignedInt, IsDictOf(IsStr, IsUnsignedInt), StringIn(
("auto", ))),
"--keep-ambigious-genotypes":
IsNone,
"--min-quality":
IsUnsignedInt,
"--min-allele-frequency":
IsFloat,
"--min-mapping-quality":
IsUnsignedInt,
"--min-read-depth":
IsUnsignedInt,
"--max-read-depth":
IsUnsignedInt,
"--min-num-alt-bases":
IsUnsignedInt,
ValuesSubsetOf(("Raw BAM", "Realigned BAM", "Coverage", "Summary",
"mapDamage", "Depths", "DuplicateHist")),
default=["Realigned BAM", "Coverage", "Summary", "mapDamage",
"Depths"]),
}
_VALIDATION = {
"Options": _VALIDATION_OPTIONS,
"Prefixes": {
_VALID_PREFIX_NAME: {
"Path": _VALID_PREFIX_PATH,
"Label": ValueIn(("nuclear", "mitochondrial", "chloroplast",
"plasmid", "bacterial", "viral")),
"RegionsOfInterest": IsDictOf(IsStr, IsStr),
},
},
_VALID_TARGET_NAME: { # Target
_VALID_TARGET_NAME: { # Sample
_VALID_TARGET_NAME: { # Library
_VALID_TARGET_NAME: Or(IsStr, IsDictOf(IsStr, IsStr)),
"Options": WithoutDefaults(_VALIDATION_OPTIONS),
},
"Options": WithoutDefaults(_VALIDATION_OPTIONS),
},
"Options": WithoutDefaults(_VALIDATION_OPTIONS),
},
},
"Filter Singletons" : {
IsStr : IsListOf(IsStr),
},
},
"Genotyping" : {
"Default" : OneOf("random", "samtools", case_sensitive = False),
"Padding" : IsInt,
"Indels" : IsBoolean,
AnyOf("MPileup", "BCFTools", "Random") : {
IsStrWithPrefix("-") : CLI_PARAMETERS,
},
"VCF_Filter" : {
"Mappability" : IsStr,
"MaxReadDepth" : Or(IsUnsignedInt, IsDictOf(IsStr, IsInt)),
IsStrWithPrefix("-") : CLI_PARAMETERS,
},
},
"MSAlignment" : {
"Enabled" : IsBoolean,
"Default" : AnyOf("mafft", case_sensitive = False),
"MAFFT" : {
"Algorithm" : AnyOf("auto", "g-ins-i", case_sensitive = False), # TODO
},
},
"Phylogenetic Inference" : {
"ExcludeGroups" : IsListOf(IsStr),
"Default" : AnyOf("raxml", "raxml-light", "examl", case_sensitive = False),
"ExaML" : {
"Threads" : IsInt,