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_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 type_to_wdl(cls,
typ: cli_types.CliType,
optional: bool = False) -> WdlType:
if isinstance(typ, cli_types.CliString):
return WdlType(PrimitiveType(PrimitiveType.kString),
optional=optional)
elif isinstance(typ, cli_types.CliFloat):
return WdlType(PrimitiveType(PrimitiveType.kFloat),
optional=optional)
elif isinstance(typ, cli_types.CliBoolean):
return WdlType(PrimitiveType(PrimitiveType.kBoolean),
optional=optional)
elif isinstance(typ, cli_types.CliInteger):
return WdlType(PrimitiveType(PrimitiveType.kInt),
optional=optional)
elif isinstance(typ, cli_types.CliFile):
return WdlType(PrimitiveType(PrimitiveType.kFile),
optional=optional)
elif isinstance(typ, cli_types.CliDir):
return WdlType(PrimitiveType(PrimitiveType.kDirectory),
optional=optional)
elif isinstance(typ, cli_types.CliTuple):
if typ.homogenous:
return WdlType(
ArrayType(cls.type_to_wdl(typ.values[0]),
requires_multiple=not optional))
else:
return WdlType(
ArrayType(
cls.type_to_wdl(lowest_common_type(typ.values)),
requires_multiple=not optional,
))
elif isinstance(typ, cli_types.CliList):
return WdlType(
ArrayType(cls.type_to_wdl(typ.value),
requires_multiple=not optional))
elif isinstance(typ, cli_types.CliEnum):
return WdlType(PrimitiveType(PrimitiveType.kString),
optional=optional)
else:
return WdlType(PrimitiveType(PrimitiveType.kString),
optional=optional)
def wdl(self, has_default=False) -> WdlType:
qm = self._question_mark_if_optional(has_default)
return WdlType.parse_type(
NativeTypes.map_to_wdl(self.primitive()) + qm)