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(
"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,
))
# t is the task
t.command = command
print(t.get_string())
def test_meta_string(self):
w = Task("meta_string", meta=Meta(author="illusional"))
expected = """\
task meta_string {
meta {
author: "illusional"
}
}"""
derived_workflow_only = "".join(
w.get_string().splitlines(keepends=True)[2:])
self.assertEqual(expected, derived_workflow_only)
def test_parameter_meta_scalar(self):
w = Task("param_meta_scalar", parameter_meta=ParameterMeta(test=42))
expected = """\
task param_meta_scalar {
parameter_meta {
test: 42
}
}"""
derived_workflow_only = "".join(
w.get_string().splitlines(keepends=True)[2:])
self.assertEqual(expected, derived_workflow_only)
def test_meta_scalar(self):
w = Task("meta_scalar", meta=Meta(arbitrary_scalar=42))
expected = """\
task meta_scalar {
meta {
arbitrary_scalar: 42
}
}"""
derived_workflow_only = "".join(
w.get_string().splitlines(keepends=True)[2:])
self.assertEqual(expected, derived_workflow_only)
def test_meta_bool(self):
w = Task("meta_scalar", meta=Meta(pos=True, neg=False))
expected = """\
task meta_scalar {
meta {
pos: true
neg: false
}
}"""
derived_workflow_only = "".join(
w.get_string().splitlines(keepends=True)[2:])
self.assertEqual(expected, derived_workflow_only)
def test_parameter_meta_string(self):
w = Task("param_meta_string",
parameter_meta=ParameterMeta(other="string value"))
expected = """\
task param_meta_string {
parameter_meta {
other: "string value"
}
}"""
derived_workflow_only = "".join(
w.get_string().splitlines(keepends=True)[2:])
self.assertEqual(expected, derived_workflow_only)
def save_to_string(self, cmd: Command) -> str:
inputs: List[CliArgument] = [*cmd.named] + (
[] if self.ignore_positionals else [*cmd.positional])
names = self.choose_variable_names(inputs)
tool = Task(
name=self.make_task_name(cmd),
command=self.make_command(cmd, names),
version="1.0",
inputs=self.make_inputs(names),
parameter_meta=self.make_parameter_meta(names),
)
return tool.get_string()
def test_call_scatter(self):
sc = WorkflowScatter(
"i",
"integers",
[
WorkflowCall(Task("task1").name, inputs_map={"num": "i"}),
WorkflowCall(Task("task2").name,
inputs_map={"num": "task1.output"}),
],
)
print(sc.get_string(indent=0))
print(sc.get_string(indent=1))
print(sc.get_string(indent=2))
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_parameter_meta_obj(self):
w = Task(
"param_meta_obj",
parameter_meta=ParameterMeta(
obj_value=ParameterMeta.ParamMetaAttribute(
help="This is help text", scalar=96)),
)
expected = """\
task param_meta_obj {
parameter_meta {
obj_value: {help: "This is help text", scalar: 96}
}
}"""
derived_workflow_only = "".join(
w.get_string().splitlines(keepends=True)[2:])
self.assertEqual(expected, derived_workflow_only)
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 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
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