def test_process_makefile__dict_keys_not_found():
def _dict_keys_missing(current, specs):
assert_raises(MakefileError, process_makefile, current, specs)
# String keys
yield _dict_keys_missing, {"C": 7}, {"A": IsInt, "B": IsInt}
# Spec keys
yield _dict_keys_missing, {1.3: "Abc"}, {IsStr: IsInt, IsInt: IsStr}
# Spec keys, instantiated
yield _dict_keys_missing, {1.3: "Abc"}, {IsStr(): IsInt, IsInt: IsStr()}
# Mixed keys, spec matches
yield _dict_keys_missing, {"C": 14}, {IsInt: IsInt, "A": IsInt}
yield _dict_keys_missing, {"A": 23}, {}
def test_process_makefile__dict_keys_found():
def _dict_keys_found(current, specs):
process_makefile(current, specs)
# String keys
yield _dict_keys_found, {"B": 7}, {"A": IsInt, "B": IsInt}
# Spec keys
yield _dict_keys_found, {1: "Abc"}, {IsStr: IsInt, IsInt: IsStr}
# Spec keys, instantiated
yield _dict_keys_found, {1: "Abc"}, {IsStr(): IsInt, IsInt: IsStr()}
# Mixed keys, spec matches
yield _dict_keys_found, {3: 14}, {IsInt: IsInt, "A": IsInt}
# Mixed keys, key matches
yield _dict_keys_found, {"A": 23}, {IsInt: IsInt, "A": IsInt}
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_is_str__default_set__valid_value():
spec = IsStr(default="abc")
assert_equal(spec.default, "abc")
def test_is_str__default_not_set():
spec = IsStr()
assert_is(spec.default, DEFAULT_NOT_SET)
def test_is_str__custom_description():
custom_desc = "a ball of string"
spec = IsStr(description=custom_desc)
assert_equal(spec.description, custom_desc)
def test_is_str__default_description():
spec = IsStr()
assert_equal(spec.description, "a non-empty string")
def _reject_not_str(value):
spec = IsStr()
assert_raises(MakefileError, spec, _DUMMY_PATH, value)
def test_is_str__rejects_empty_str():
spec = IsStr()
assert_raises(MakefileError, spec, _DUMMY_PATH, "")
def test_is_str__accepts_unicode_str():
spec = IsStr()
spec(_DUMMY_PATH, u"def")
def test_is_str__accepts_standard_str():
spec = IsStr()
spec(_DUMMY_PATH, "abc")
# Recursive definition of sample tree
_VALIDATION_SUBSAMPLE_KEY = And(StringStartsWith("<"), StringEndsWith(">"))
_VALIDATION_SAMPLES_KEY = And(IsStr, Not(_VALIDATION_SUBSAMPLE_KEY))
_VALIDATION_SAMPLES = {
_VALIDATION_SAMPLES_KEY: {
"GenotypingMethod":
StringIn(("reference sequence", "random sampling", "samtools"),
default="samtools"),
"SpeciesName":
IsStr, # Not used; left for backwards compatibility
"CommonName":
IsStr, # Not used; left for backwards compatibility
"Gender":
IsStr(default=REQUIRED_VALUE),
}
}
_VALIDATION_SAMPLES[_VALIDATION_SUBSAMPLE_KEY] = _VALIDATION_SAMPLES
# Genotyping settings; note that explicit lists must not be used here, to allow
# 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),
},
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))
# 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":
