def convert_transformations_to_workflow(transformations) -> Workflow:
transformations: List[JanisTransformation] = transformations
initial_tr: JanisTransformation = transformations[0]
final_tr: JanisTransformation = transformations[-1]
w = WorkflowBuilder(
f"convert_{initial_tr.type1.name().lower()}_to_{final_tr.type2.name().lower()}"
)
prev_input = w.input(f"inp_{initial_tr.type1.name().lower()}",
initial_tr.type1)
for transform in transformations:
stpid = f"transform_{transform.type1.name().lower()}_to_{transform.type2.name().lower()}"
stp_inputs = {
**(transform.tool.connections or {}),
transform.relevant_tool_input:
prev_input,
}
prev_input = w.step(
stpid,
transform.tool(**stp_inputs))[transform.relevant_tool_output]
w.output("out", final_tr.type2, source=prev_input, output_name=False)
return w
def wrapped_in_wf(self):
from copy import copy
from janis_core.workflow.workflow import WorkflowBuilder
wf = WorkflowBuilder(self.id() + "Wf")
inpmap = {}
for i in self.inputs():
if isinstance(i.input_type, Filename):
intp = String(optional=True)
else:
intp = copy(i.input_type)
if i.default:
intp.optional = True
inpmap[i.id()] = wf.input(i.id(), intp)
stp = wf.step(self.tool().lower(), self(**inpmap))
for o in self.outputs():
wf.output(o.id(), source=stp[o.id()])
return wf
def test_workflow(self):
w = WorkflowBuilder("test_container_workflow")
w.input("inp", String)
w.input("aInp", Array(String))
w.step("stp1", TestTool(testtool=w.inp))
w.step("stp1_v2", TestToolV2(testtool=w.inp))
w.step("stp2", ArrayTestTool(inps=w.aInp))
cons = w.containers()
self.assertSetEqual(
{
"ArrayStepTool", "TestTranslationtool",
"TestTranslationtool_v0_0_2"
},
set(cons.keys()),
)
self.assertIsNone(cons["ArrayStepTool"])
self.assertEqual("ubuntu:latest", cons["TestTranslationtool"])
self.assertEqual("ubuntu:latest", cons["TestTranslationtool_v0_0_2"])
def test_switch(self):
from janis_unix import Echo, Cat
w = WorkflowBuilder("switchTest")
w.input("inp", int, value=2)
w.input("inp1", str, value="Hello")
w.input("inp2", str, value="Hi there")
w.conditional(
"echoswitch",
[
(w.inp > 1, Echo(inp=w.inp1)),
(w.inp.equals(1), Echo(inp="tasy case")),
Echo(inp=w.inp2),
],
)
w.output("out", source=w.echoswitch)
_, wdl_tools = WdlTranslator.translate_workflow(w)
expected = """\
version development
import "echo_v1_0_0.wdl" as E
workflow echoswitch {
input {
Int cond_inp
String switch_case_1_inp
String? switch_case_2_inp = "tasy case"
String switch_case_3_inp
}
if ((cond_inp > 1)) {
call E.echo as switch_case_1 {
input:
inp=switch_case_1_inp
}
}
if (((cond_inp == 1) && !((cond_inp > 1)))) {
call E.echo as switch_case_2 {
input:
inp=select_first([switch_case_2_inp, "tasy case"])
}
}
if (!(((cond_inp > 1) || (cond_inp == 1)))) {
call E.echo as switch_case_3 {
input:
inp=switch_case_3_inp
}
}
output {
File out = select_first([switch_case_1.out, switch_case_2.out, switch_case_3.out])
}
}"""
echoswitch = wdl_tools["echoswitch"].get_string()
self.assertEqual(expected, echoswitch)
def test_1(self):
from janis_unix import Echo, Cat
w = WorkflowBuilder("conditionalTest")
w.input("inp", int, value=1)
w.input("name", str, value="Michael")
w.step("echo", Echo(inp=w.name), when=w.inp > 1)
w.step("cat",
Cat(file=w.echo.out),
when=w.echo.out.equals("Hello, Michael"))
w.output("out", source=w.echo.out)
w.translate(
"wdl" # to_disk=True, export_path="~/Desktop/tmp/{name}", validate=True
)