def test_expression_default(self):
wf = WorkflowBuilder("test_expression_defaults")
wf.input("inp", Optional[str])
wf.step(
"echo",
EchoTestTool(inp="Hello, " +
If(IsDefined(wf.inp), wf.inp, ", Michael!")),
)
wf.output("out", source=wf.echo)
wf.translate("cwl")
def test_workflow_string_not_null(self):
w = WorkflowBuilder("wf")
w.input("inp", Optional[str])
w.output("out", source=w.inp.assert_not_null())
cwltool = w.translate("cwl", allow_empty_container=True, to_console=False)[0]
print(cwltool)
def test_with_str_default(self):
w = WorkflowBuilder("wf")
w.input("inp", str, default="hello")
w.output("out", source=w.inp)
out, _, _ = w.translate("wdl", to_console=False)
expected = """\
version development
workflow wf {
input {
String? inp
}
output {
String out = select_first([inp, "hello"])
}
}"""
self.assertEqual(expected, out)
def test_with_int_default(self):
w = WorkflowBuilder("wf")
w.input("inp", int, default=0)
w.output("out", source=w.inp)
out, _, _ = w.translate("wdl", to_console=False)
expected = """\
version development
workflow wf {
input {
Int? inp
}
output {
Int out = select_first([inp, 0])
}
}"""
self.assertEqual(expected, out)
def test_simple(self):
w = WorkflowBuilder("wf")
w.input("inp", str)
w.output("out", source=w.inp)
out, _, _ = w.translate("wdl", to_console=False)
expected = """\
version development
workflow wf {
input {
String inp
}
output {
String out = inp
}
}"""
self.assertEqual(expected, out)
def test_array_step_input(self):
wf = WorkflowBuilder("cwl_test_array_step_input")
wf.input("inp1", Optional[str])
wf.input("inp2", Optional[str])
wf.step(
"print",
ArrayTestTool(
inps=[
If(IsDefined(wf.inp1), wf.inp1, "default1"),
If(IsDefined(wf.inp2), wf.inp2 + "_suffix", ""),
]
),
),
wf.output("out", source=wf.print)
ret, _, _ = wf.translate("cwl", allow_empty_container=True, to_console=False)
self.maxDiff = None
self.assertEqual(cwl_arraystepinput, ret)
def test_basic(self):
w = WorkflowBuilder("wb")
w.input("inp", str)
w.step("echo", SingleTestTool(inputs=w.inp))
w.step("echo_2", SingleTestTool(inputs=w.inp))
wf, _, _ = w.translate(
"wdl",
to_console=False,
with_resource_overrides=True,
allow_empty_container=True,
)
_tooldef = """\
workflow wb {
input {
String inp
Int? echo_runtime_memory
Int? echo_runtime_cpu
String echo_runtime_disks
Int? echo_2_runtime_memory
Int? echo_2_runtime_cpu
String echo_2_runtime_disks
}
call T.TestStepTool as echo {
input:
inputs=inp,
runtime_memory=echo_runtime_memory,
runtime_cpu=echo_runtime_cpu,
runtime_disks=echo_runtime_disks
}
call T.TestStepTool as echo_2 {
input:
inputs=inp,
runtime_memory=echo_2_runtime_memory,
runtime_cpu=echo_2_runtime_cpu,
runtime_disks=echo_2_runtime_disks
}
}"""
self.assertEqual(_tooldef, "\n".join(wf.split("\n")[4:]))
@staticmethod
def base_command():
return "echo" # non functional tool
def inputs(self) -> List[ToolInput]:
return [ToolInput("inp", DataTypeWithSecondary())]
def outputs(self) -> List[ToolOutput]:
return [
ToolOutput("out",
DataTypeWithSecondary(),
glob=InputSelector("inp"))
]
if __name__ == "__main__":
w = WorkflowBuilder("test_workflow")
w.input("inp", DataTypeWithSecondary)
w.step("stp", ToolThatAcceptsAndReturnsSecondary(inp=w.inp))
w.output("out", source=w.stp)
w.translate("wdl")
w2 = WorkflowBuilder("scattered_test_workflow")
w2.input("inp", Array(DataTypeWithSecondary), default=["path/to/file.ext"])
w2.step("stp",
ToolThatAcceptsAndReturnsSecondary(inp=w2.inp),
scatter="inp")
w2.output("out", source=w2.stp)
w2.translate("wdl")
from janis_core import (
WorkflowBuilder,
Array,
String,
ScatterDescription,
StringFormatter,
)
from janis_unix import Echo
w = WorkflowBuilder("scatterlabel_test")
w.input("inps", Array(String), value=["test1,1", "test2,2", "test3,3"])
w.step(
"print",
Echo(inp=w.inps),
scatter=ScatterDescription(["inp"], labels=["Printing 1", "Printing 2"]),
)
w.output("out", source=w.print, extension=".csv")
if __name__ == "__main__":
w.translate("cwl")
