def test_bedtools_window_sm():
"""
These two flags have almost the same name, and almost the same description
"""
flags = [
Flag(
synonyms=["-sm"],
description=
"Only report hits in B that overlap A on the _same_ strand.",
args=EmptyFlagArg(),
),
Flag(
synonyms=["-sm"],
description=
"Only report hits in B that overlap A on the _opposite_ strand.",
args=EmptyFlagArg(),
),
Flag(
synonyms=["-c"],
description=
"For each entry in A, report the number of overlaps with B.",
args=EmptyFlagArg(),
),
]
args = WrapperGenerator().choose_variable_names(flags)
assert len(set([arg.name for arg in args])) == 3
def test_same_arg():
"""
Normally we ignore one-character flag names, and instead try to read their descriptions for a more informative name.
However, if the descriptions are identical to each other, we have to fall back to the description
"""
flags = [
Flag(synonyms=["-a"], description="", args=SimpleFlagArg("SomeThing")),
Flag(synonyms=["-b"], description="", args=SimpleFlagArg("SomeThing")),
]
names = WrapperGenerator().choose_variable_names(flags)
assert names[0].name == "a"
assert names[1].name == "b"
def test_snake_short(snake_gen):
flag = Flag(
synonyms=["-t"], description="number of threads [1]", args=EmptyFlagArg()
)
names = snake_gen.choose_variable_names([flag], length=2)
assert "number" in names[0].name
assert "threads" in names[0].name
def test_snake_long(snake_gen):
flag = Flag(
synonyms=["-g", "--genomepaths", "--genomefolders"],
description="number of threads [1]",
args=EmptyFlagArg(),
)
names = snake_gen.choose_variable_names([flag], length=2)
assert names[0].name == "genome_folders"
def test_name_to_words_symbol(gen):
"""
Check that we can get an argument name even if the argument's flag is a symbol
"""
arg = Flag(
synonyms=["-@"],
description="Number of additional threads to use",
args=EmptyFlagArg(),
)
name = gen.choose_variable_names([arg])[0].name
assert name == "at"
def test_samtools_dict_output():
gen = WdlGenerator()
arg = Flag(
synonyms=["-o", "--output"],
description="file to write out dict file [stdout]",
args=SimpleFlagArg(name="str"),
)
name = gen.choose_variable_names([arg])[0].name
# The WDL converter should avoid naming a variable "output" since that's a WDL keyword
assert name != "output"
# Also, since we have a description, the generator shouldn't choose the lazy option of var_output
assert name != "var_output"
def test_name_to_words(gen):
"""
Check that we can get an argument name even if the argument's flag is a symbol
"""
arg = Flag(
synonyms=["--genomepaths"],
description="",
args=EmptyFlagArg(),
)
name = gen.choose_variable_names([arg])[0].name
assert "genome" in name
assert "paths" in name
def visit_short_flag_list(s, loc, toks):
return [
Flag.from_synonyms(
[FlagSynonym(name="-" + flag, argtype=EmptyFlagArg())],
description=None) for flag in toks[1:]
]
options_placeholder = (Regex(
"options?", flags=re.IGNORECASE).suppress().setName("OptionsPlaceholder"))
list_element = (
(OneOrMore(options_placeholder ^ mandatory_element ^ variable_element) +
Literal(".")[2, 3] +
Optional(options_placeholder ^ mandatory_element ^ variable_element)
).setParseAction(visit_list_element).setName("list_element"))
"""
When one or more arguments are allowed, e.g. "<in2.bam> ... <inN.bam>"
"""
usage_flag = (And([flag_with_arg
]).setParseAction(lambda s, loc, toks: Flag.from_synonyms(
toks, description="")).setName("usage_flag"))
usage_element <<= Or([
optional_section,
list_element,
# short_flag_list,
usage_flag,
variable_element,
options_placeholder,
mandatory_element,
]).setName("usage_element")
stack = [1]
def visit_usage(s, loc, toks):
def test_camel_short(camel_gen):
flag = Flag(
synonyms=["-t"], description="number of threads [1]", args=EmptyFlagArg()
)
names = camel_gen.choose_variable_names([flag], length=3)
assert names[0].name == "numberOfThreads"
def test_bwt2sa_i(gen):
arg = Flag(synonyms=["-i"], description="", args=SimpleFlagArg(name="32"))
name = gen.choose_variable_names([arg])[0].name
# 32 isn't a valid variable name, so the only option here is to use the letter i
assert name == "i"