def test_from_bash_check_io_array(hint, req, sec):
tool = cwl.CommandLineTool.from_bash(
'echo $IN',
inputs={'IN': cwl.Array(hint, required=req)},
outputs={'OUT': cwl.Array(hint, required=req)},
secondary_files={'IN': sec})
assert tool.inputs[0].type == TypeFactory.create(
cwl.Array(hint, required=req), True)
assert tool.outputs[0].type == TypeFactory.create(
cwl.Array(hint, required=req), False)
assert tool.inputs[0].secondary_files == sec
def test_outputs_from_f_arr(tool, hint):
f = make_f(int, r={'y': cwl.Array(hint)})
outputs = tool._outputs_from_f(f)
o = outputs[0]
assert o['id'] == 'y'
assert type(o['type']) == cwl.Array
assert o['type'].val == hint
def test_inputs_from_f_arr(tool, hint):
f = make_f(cwl.Array(hint))
inputs = tool._inputs_from_f(f)
i = inputs[0]
assert i['id'] == 'x'
assert type(i['type']) == cwl.Array
assert i['type'].val == hint
def inputs():
return dict(
input_str=cwl.String(),
input_int=cwl.Int(),
input_bool=cwl.Bool(),
input_float=cwl.Float(),
input_enum=cwl.Enum(['a', 'b', 'c']),
input_record=cwl.Record(dict(k1=cwl.String())),
input_array=cwl.Array(cwl.Int()),
input_no_type=cwl.Any(),
input_union=cwl.Union([cwl.Int(), cwl.String()]),
input_nonreq_primitive=cwl.String(),
input_nonreq_none=cwl.String(),
input_nonreq_object=cwl.Enum(['a', 'b', 'c'])
)
from sbg import cwl
with cwl.workflow('scatter_single.cwl', 'w') as wf:
t1 = cwl.ExpressionTool('$({"out": inputs.word })', id='expr_tool1')
t1.add_input(cwl.String(required=True), id='word', label='Word')
t1.add_output(cwl.String(required=True), id='out', label='Word out')
t2 = cwl.ExpressionTool(
'$({"out": inputs.word.map(function(x){ return x.toLowerCase()}) })',
id='expr_tool2')
t2.add_input(cwl.Array(cwl.String(), required=True),
id='word',
label='Word')
t2.add_output(cwl.Array(cwl.String(), required=True),
id='out',
label='Word out')
wf.add_step(t1, expose=['word'], scatter=['word'])
wf.add_step(t2, expose=['out'])
wf.add_connection('expr_tool1.out', 'expr_tool2.word')
wf.add_requirement(cwl.InlineJavascript())
wf.add_requirement(cwl.ScatterFeature())
def test_add_output_arr(cls, hint, required):
obj = cls()
t = cwl.Array(hint(), required=required)
o = obj.add_output(t)
assert o.type == TypeFactory.create(t, False)
def test_add_input_arr(cls, hint, required):
obj = cls()
t = cwl.Array(hint(), required=required)
i = obj.add_input(t)
assert i.type == TypeFactory.create(t, True)
Resource(),
Docker(docker_pull='something'), InlineJavascript(),
EnvVar(EnvironmentDef('foo', 'bar')),
InitialWorkDir([Dirent('hello world', 'foo.txt')]),
EnvVar(EnvironmentDef('foo', 'bar'))
])
def test_find_requirement(req, cls):
obj = cls()
obj.add_requirement(req)
assert obj.find_requirement(req.class_) == req
@pytest.mark.parametrize('cls', [CommandLineTool, Workflow])
@pytest.mark.parametrize('type', [
cwl.String(), cwl.Int(), cwl.Float(), cwl.Bool(), cwl.Record(), cwl.Enum(),
cwl.Array(cwl.Int())
])
def test_get_port(type, cls):
obj = cls()
i = obj.add_input(type, id='in')
o = obj.add_output(type, id='out')
assert obj.get_port('in') == i
assert obj.get_port('out') == o
@pytest.mark.parametrize('cls', [CommandLineTool, Workflow])
@pytest.mark.parametrize('type', [
cwl.String(), cwl.Int(), cwl.Float(), cwl.Bool(), cwl.Record(), cwl.Enum(),
cwl.Array(cwl.Int())
])
def outputs():
return dict(
out_str=cwl.String(),
out_glob_star=cwl.Array(cwl.File(), glob='*.txt'),
out_glob=cwl.File(glob="some_name")
)