def test_input_value_string_nostringenv(self):
self.assertEqual(
'"TestString"',
wdl.get_input_value_from_potential_selector_or_generator(
"TestString", None, string_environment=False
),
)
def test_input_value_int_nostringenv(self):
self.assertEqual(
42,
wdl.get_input_value_from_potential_selector_or_generator(
42, None, string_environment=False
),
)
def test_input_value_none_stringenv(self):
self.assertEqual(
None,
wdl.get_input_value_from_potential_selector_or_generator(
None, None, string_environment=True
),
)
def test_resolve_filename_in_inpselect(self):
fn = Filename(extension=".ext")
ti = {"ti": ToolInput("ti", fn)}
b = StringFormatter("fn: {place}", place=InputSelector("ti"))
res = wdl.get_input_value_from_potential_selector_or_generator(b, ti)
self.assertEqual(
f'fn: ~{{select_first([ti, "{fn.generated_filename()}"])}}', res)
def test_input_value_filename_nostringenv(self):
fn = Filename()
self.assertEqual(
'"%s"' % fn.generated_filename(),
wdl.get_input_value_from_potential_selector_or_generator(
fn, None, string_environment=False),
)
def test_input_value_filename_stringenv(self):
import uuid
fn = Filename(guid=str(uuid.uuid4()))
self.assertEqual(
fn.generated_filename(),
wdl.get_input_value_from_potential_selector_or_generator(
fn, None, string_environment=True
),
)
def test_input_value_wdl_callable(self):
class CallableWdl:
def wdl(self):
return "unbelievable"
self.assertEqual(
"unbelievable",
wdl.get_input_value_from_potential_selector_or_generator(
CallableWdl(), None),
)
def test_input_value_cpuselect_stringenv(self):
# CpuSelector relies on their being a runtime_cpu attribute,
# this test will assume it's present, and '' will test ensure
# that it is actually present
ti = {"runtime_cpu": ToolInput("runtime_cpu", Int(), default=1)}
inp = CpuSelector()
self.assertEqual(
"~{select_first([runtime_cpu, 1])}",
wdl.get_input_value_from_potential_selector_or_generator(
inp, ti, string_environment=True),
)
def test_string_formatter_two_param(self):
# vardict input format
d = {
"tumorInputName": ToolInput("tumorInputName", String()),
"normalInputName": ToolInput("normalInputName", String()),
}
b = StringFormatter(
"{tumorName}:{normalName}",
tumorName=InputSelector("tumorInputName"),
normalName=InputSelector("normalInputName"),
)
res = wdl.get_input_value_from_potential_selector_or_generator(b, d)
self.assertEqual("${tumorInputName}:${normalInputName}", res)
def test_string_formatter_optional_inpselect_with_default(self):
ti = {"ti": ToolInput("ti", String(optional=True), default="hi")}
b = StringFormatter("{place} michael", place=InputSelector("ti"))
res = wdl.get_input_value_from_potential_selector_or_generator(b, ti)
self.assertEqual('${if defined(ti) then ti else "hi"} michael', res)
def test_string_formatter_one_input_selector_param(self):
d = {"random_input": ToolInput("random_input", String())}
b = StringFormatter("an input {arg}", arg=InputSelector("random_input"))
res = wdl.get_input_value_from_potential_selector_or_generator(b, d)
self.assertEqual("an input ${random_input}", res)
def test_string_formatter_one_string_param(self):
b = StringFormatter("there's {one} arg", one="a string")
res = wdl.get_input_value_from_potential_selector_or_generator(b, None)
self.assertEqual("there's a string arg", res)
def test_string_formatter(self):
b = StringFormatter("no format")
res = wdl.get_input_value_from_potential_selector_or_generator(b, None)
self.assertEqual("no format", res)
