def test_readme_task(self):
t = Task("task_name")
t.inputs.append(Input(WdlType.parse_type("String"), "taskGreeting"))
# command in next section
t.outputs.append(
Output(WdlType.parse_type("File"), "standardOut", "stdout()"))
command = Task.Command("echo")
command.inputs.append(
Task.Command.CommandInput.from_fields(
"taskGreeting",
optional=False,
position=None,
prefix="-a",
separate_value_from_prefix=True,
default=None,
))
command.inputs.append(
Task.Command.CommandInput.from_fields(
"otherInput",
optional=True,
position=2,
prefix="optional-param=",
separate_value_from_prefix=False,
default=None,
))
command = Task.Command("echo")
command.inputs.append(
Task.Command.CommandInput.from_fields(
"taskGreeting",
optional=False,
position=None,
prefix="-a",
separate_value_from_prefix=True,
default=None,
))
command.inputs.append(
Task.Command.CommandInput.from_fields(
"otherInput",
optional=True,
position=2,
prefix="optional-param=",
separate_value_from_prefix=False,
default=None,
))
# t is the task
t.command = command
print(t.get_string())
def test_readme_example(self):
command = Task.Command("echo")
command.inputs.append(
Task.Command.CommandInput(
"taskGreeting",
optional=False,
position=None,
prefix="-a",
separate_value_from_prefix=True,
default=None,
))
command.inputs.append(
Task.Command.CommandInput(
"otherInput",
optional=True,
position=2,
prefix="optional-param=",
separate_value_from_prefix=False,
default=None,
))
output = command.get_string()
expected = '''\
echo \\
-a ~{taskGreeting} \\
~{'"optional-param=' + otherInput + '"'}'''
# t is the task
self.assertEqual(expected, output)
# Check that it's also valid WDL
parse_miniwdl_token('command2', 'command <<<\n' + output + '\n>>>')
def test_readme_example(self):
command = Task.Command("echo")
command.inputs.append(
Task.Command.CommandInput.from_fields(
"taskGreeting",
optional=False,
position=None,
prefix="-a",
separate_value_from_prefix=True,
default=None,
))
command.inputs.append(
Task.Command.CommandInput.from_fields(
"otherInput",
optional=True,
position=2,
prefix="optional-param=",
separate_value_from_prefix=False,
default=None,
))
expected = """\
echo \\
-a ~{taskGreeting} \\
~{if defined(otherInput) then ('"' + "optional-param=" + otherInput + '"') else ""}"""
# t is the task
self.assertEqual(expected, command.get_string())
def test_simple_command(self):
command = Task.Command("egrep")
command.inputs.append(Task.Command.CommandInput("pattern"))
command.inputs.append(Task.Command.CommandInput("in"))
expected = """\
egrep \\
~{pattern} \\
~{in}"""
self.assertEqual(expected, command.get_string(0))
def make_command(self, cmd: Command,
inputs: List[NamedArgument]) -> Task.Command:
return Task.Command(
command=" ".join(cmd.command),
inputs=[
flag_to_command_input(input, self) for input in inputs
if isinstance(input.arg, Positional)
],
arguments=[
flag_to_command_input(input, self) for input in inputs
if isinstance(input.arg, Flag)
],
)
def test_simple_task(self):
# Task based on: https://github.com/openwdl/wdl/blob/master/versions/draft-2/SPEC.md#introduction
t = Task("hello",
runtime=Task.Runtime(docker="broadinstitute/my_image"))
t.inputs.extend([
Input(WdlType.parse_type("String"), "pattern"),
Input(WdlType.parse_type("File"), "in"),
])
t.outputs.append(
Output(WdlType.parse_type("Array[String]"), "matches",
"read_lines(stdout())"))
t.command = Task.Command(
"egrep",
inputs=[Task.Command.CommandInput.from_input(i) for i in t.inputs])
print(t.get_string())
return t
def test_hello_tasks():
# https://github.com/openwdl/wdl/#specifying-inputs-and-using-declarations
t1 = Task(
"hello",
inputs=[Input(String, "name"),
Input(String, "salutation")],
outputs=[Output(String, "response", "read_string(stdout())")],
)
t1.command = Task.Command(
"echo",
inputs=[
Task.Command.CommandInput.from_input(t1.inputs[i], position=i)
for i in range(2)
],
)
print(t1.get_string())
return t1
