def test_auto_expose_all(wf):
t = CommandLineTool(id='t')
input = t.add_input(cwl.String(), 'input')
output = t.add_output(cwl.String(), 'output')
wf.add_step(t)
assert wf.inputs == [
WorkflowInput(id='input',
label='input',
type=Workflow.set_required(Primitive.STRING, False))
]
assert wf.outputs == [
WorkflowOutput(id='output',
label='output',
output_source='{}/{}'.format(t.id, output.id),
type=Workflow.set_required(Primitive.STRING, False))
]
assert wf.steps[0] == Step(id=t.id,
in_=[StepInput(input.id, source=input.id)],
out=[StepOutput(output.id)],
run=t)
def test_get_step(wf):
t1 = CommandLineTool(id='t1')
t2 = CommandLineTool(id='t2')
wf.add_step(t1)
wf.add_step(t2)
assert wf.get_step('t1').run == t1
assert wf.get_step('t2').run == t2
def test_add_step(wf):
t1 = CommandLineTool(id='t1')
t2 = CommandLineTool(id='t2')
t3 = Workflow()
wf.add_step(t1)
wf.add_step(t2)
wf.add_step(t3)
assert wf.steps[0] == Step(t1.id, [], [], t1)
assert wf.steps[1] == Step(t2.id, [], [], t2)
assert wf.steps[2] == Step(t3.id, [], [], t3)
def test_add_connection_wf_input(wf):
wf.add_input(cwl.String(), 'input_str')
t1 = CommandLineTool(id='t1')
t1.add_input(cwl.String(), 'input_str')
wf.add_step(t1, expose=[])
wf.add_connection('input_str', 't1.input_str')
assert wf.steps[0].in_ == [StepInput('input_str', source='input_str')]
def test_scatter_single_check_input(wf, hint, required):
t1 = CommandLineTool(id='t1')
ihint = hint(required=required)
t = TypeFactory.create(ihint, True)
t1.add_input(ihint, 'input')
step1 = wf.add_step(t1, expose=['input'])
wf.scatter(step1, ['input'], None)
assert isinstance(wf.inputs[0].type, InputArray)
if is_primitive(t) and not ihint.required:
t = [Primitive.NULL, t.rstrip('?')]
assert wf.inputs[0].type.items_ == t
def test_add_connection_wf_output(wf):
wf.add_output(cwl.String(), 'output_str')
t1 = CommandLineTool(id='t1')
t1.add_output(cwl.String(), 'output_str')
wf.add_step(t1, expose=[])
wf.add_connection('t1.output_str', 'output_str')
assert wf.outputs[0] == WorkflowOutput(id='output_str',
output_source='t1/output_str',
type=set_required(
Primitive.STRING, False))
def test_expose_except(wf):
t = CommandLineTool(id='test')
t.add_input(cwl.Int(default=10, required=True), id='x')
t.add_input(cwl.String(), id='y')
t.add_output(cwl.File(glob='something', required=True), id='out')
wf.add_step(t, expose_except=['y', 'out'])
assert wf.inputs == [WorkflowInput(id='x', label='x', type=Primitive.INT)]
assert wf.outputs == []
def test_scatter_multi_check_input(wf, hint, req, method):
tool = CommandLineTool(id='t')
h = hint(required=req)
hint_type = TypeFactory.create(h, True)
inputs = [tool.add_input(h, 'input1'), tool.add_input(h, 'input2')]
step = wf.add_step(tool, expose=['input1', 'input2'])
wf.scatter(step, ['input1', 'input2'], method)
if is_primitive(hint_type) and not h.required:
hint_type = [Primitive.NULL, hint_type.rstrip('?')]
for i in inputs:
wfi = wf.get_port(i.id)
assert isinstance(wfi.type, InputArray)
assert wfi.type.items_ == hint_type
def test_scatter_multi_check_output(wf, hint, req, method):
tool = CommandLineTool(id='t')
h = hint(required=req)
inputs = [
tool.add_input(h, 'input1'),
tool.add_input(h, 'input2'),
tool.add_input(h, 'input3')
]
outputs = [tool.add_output(h, 'output1'), tool.add_output(h, 'output2')]
scatter = [i.id for i in inputs]
step = wf.add_step(tool, expose=scatter + [o.id for o in outputs])
wf.scatter(step, scatter, method)
# number of iterations
n = len(scatter) if method == ScatterMethod.NESTED_CROSSPRODUCT else 1
for o in outputs:
wfo = wf.get_port(o.id)
if req:
parent = wfo.type
for _ in range(n):
assert isinstance(parent, OutputArray)
parent = parent.items_
else:
assert Primitive.NULL in wfo.type
wfo.type.remove(Primitive.NULL)
assert len(wfo.type) == 1
parent = wfo.type[0]
for _ in range(n):
assert isinstance(parent, OutputArray)
parent = parent.items_
h.required = True
assert parent == TypeFactory.create(h, False)
def test_is_scattered(wf, hint, req, scatter):
tool = CommandLineTool(id='t')
h = hint(required=req)
tool.add_input(h, 'input1')
tool.add_input(h, 'input2')
tool.add_input(h, 'input3')
step = wf.add_step(tool, scatter=scatter)
for k in scatter:
assert step.is_scattered(k) is True
def test_scatter_single_check_output(wf, hint, req):
tool = CommandLineTool(id='t')
h = hint(required=req)
tool.add_input(h, 'input')
tool.add_output(h, 'output')
step = wf.add_step(tool, expose=['output'])
wf.scatter(step, ['input'], None)
if req:
assert isinstance(wf.outputs[0].type, OutputArray)
else:
assert Primitive.NULL in wf.outputs[0].type
wf.outputs[0].type.remove(Primitive.NULL)
assert len(wf.outputs[0].type) == 1
assert isinstance(wf.outputs[0].type[0], OutputArray)
h.required = True
assert wf.outputs[0].type[0].items_ == TypeFactory.create(h, False)
def test_add_connection_inner_nodes(wf):
t1 = CommandLineTool(id='t1')
t2 = CommandLineTool(id='t2')
t1.add_input(cwl.String(), 'input')
t1.add_output(cwl.String(), 'output')
t2.add_input(cwl.String(), 'input')
t2.add_output(cwl.String(), 'output')
wf.add_step(t1, expose=[])
wf.add_step(t2, expose=[])
wf.add_connection('t1.output', 't2.input')
assert wf.steps[0].out == [StepOutput('output')]
assert wf.steps[1].in_ == [StepInput('input', source='t1/output')]