def test_associativity(self):
""" Command construction satisfies associativity. """
expected = "fseq -d input_folder -o output -of npf input_file"
assert expected == build_command(expected.split())
assert expected == build_command([
"fseq", ("-d", "input_folder"), "-o", ("output", "-of"), "npf",
"input_file"
])
assert expected == build_command([("fseq", "-d"),
("input_folder", "-o"), "output",
"-of", ("npf", "input_file")])
def test_ignores_null_singletons(self):
""" Conditional expression for positional arg may evaluate to null. """
cmd_chunks = [
"java", ("-jar", "trimmomatic.jar"), None, ("-o", None),
"input_file.txt"
]
expected = "java -jar trimmomatic.jar input_file.txt"
assert expected == build_command(cmd_chunks)
def test_trims_spaces_from_optarg(self, expected_opt):
""" Space characters are trimmed from option and argument. """
expected_arg = "output_dir"
opt_template = " {} "
arg_template = " {} "
opt_input = opt_template.format(expected_opt)
arg_input = arg_template.format(expected_arg)
expected = "{} {}".format(expected_opt, expected_arg)
observed = build_command([(opt_input, arg_input)])
assert expected == observed
def test_conditional_argument_specification(self, arg_by_opt):
""" Null-valued options are ignored. """
optnames = ["--gsize", "--qvalue"]
program = "macs2 callpeak"
opts_text = "-f BED --nomodel"
options = [(opt, arg_by_opt[opt] if opt in arg_by_opt else None)
for opt in optnames]
cmd = build_command([program] + [opts_text] + options)
for opt in optnames:
if opt in arg_by_opt:
assert "{} {}".format(opt, arg_by_opt[opt]) in cmd
else:
assert opt not in cmd
expected_num_spaces = -1 + sum(
len(command_section) for command_section in
[program.split(" "),
opts_text.split(" "), options])
print("Expecting {} spaces in command: {}".format(
expected_num_spaces, cmd))
assert expected_num_spaces == cmd.count(" ")
def test_prohibits_container_element_with_more_than_two_items(
self, chunks):
""" Only raw strings and two-tuples are allowed. """
with pytest.raises(ValueError):
build_command(chunks)
def test_retains_non_space_whitespace(self, option, argument):
""" Command builder retains non-space whitespace (e.g., delimiter). """
assert "{} {}".format(option,
argument) == build_command([(option, argument)])
def test_trims_spaces_raw_string(self, text):
""" Space characters are trimmed from text ends. """
assert text.strip(" ") == build_command([text])
def test_single_non_null_valued_option_is_used(self, option, argument):
""" Non-null-valued option is included in command, single-spaced. """
assert "{} {}".format(option,
argument) == build_command([(option, argument)])
def test_single_null_value_option_is_omitted(self, option):
""" Null-valued option is excluded from command. """
assert "" == build_command([(option, None)])
def test_single_wrapped_string_is_unchanged(self):
""" Raw command within contained type is returned as the command. """
digits_string = "".join(random.choice(string.digits))
assert digits_string == build_command(digits_string)
def test_raw_string_is_unchanged(self):
""" Single raw text command is returned as such. """
text = "".join(random.choice(string.letters))
assert text == build_command(text)
def test_ignores_single_null(self):
""" Command builder ignores each null singleton. """
assert "" == build_command([None])
def test_requires_chunks(self, chunks):
""" Fail loudly to halt processing if no command parts are there. """
with pytest.raises(ValueError):
build_command(chunks)
