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 make_outputs(self, names: List[NamedArgument]) -> List[Output]:
ret = [
# We default to always capturing stdout
Output(data_type=File, name="out_stdout", expression="stdout()")
]
for arg in names:
typ = arg.arg.get_type()
if isinstance(typ, cli_types.CliFileSystemType) and typ.output:
ret.append(
Output(
data_type=self.type_to_wdl(typ),
name="out_" + arg.name,
expression='"${{in_{}}}"'.format(arg.name),
))
return ret
def test_readme(self):
w = Workflow("workflow_name")
w.imports.append(Workflow.WorkflowImport("tool_file", ""))
w.inputs.append(Input(WdlType.parse_type("String"), "inputGreeting"))
inputs_map = {"taskGreeting": "inputGreeting"}
w.calls.append(
WorkflowCall("Q.namspaced_task_identifier", "task_alias",
inputs_map))
w.outputs.append(
Output(WdlType.parse_type("File"), "standardOut",
"task_alias.standardOut"))
print(w.get_string())
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