def test_step_with_scattered_input_no_scatter_method(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
msgs = wf.add_input(wfmessages='string[]')
wf.echo(message=msgs, scatter='message')
wf.validate()
def test_step_with_compatible_input(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
wfmessage = wf.add_input(wfmessage='string')
echoed = wf.echo(message=wfmessage)
wf.validate()
def test_enum_as_workflow_input(self):
wf = WorkflowGenerator()
wf.add_input(input1='enum', symbols=['one', 'two', 'three'])
wf.validate()
obj = wf.to_obj()['inputs']['input1']
assert obj['type']['type'] == 'enum'
assert obj['type']['symbols'] == ['one', 'two', 'three']
def test_label_for_workflow_input(self):
wf = WorkflowGenerator()
wf.add_input(input1='string', label='test label')
wf.validate()
obj = wf.to_obj()['inputs']['input1']
assert obj['type'] == 'string'
assert obj['label'] == 'test label'
def test_optional_type(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
# This could work, if you pass a string for input, even if
# the echo step requires an input. So we expect it to work.
wfmessage = wf.add_input(message='string?')
echod = wf.echo(message=wfmessage)
wf.validate()
def test_step_with_scattered_step_output(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
msgs = wf.add_input(msgs='string[]')
echoed = wf.echo(message=msgs, scatter='message',
scatter_method='dotproduct')
wced = wf.wc(file2count=echoed, scatter='file2count',
scatter_method='dotproduct')
wf.validate()
def test_scatter_method_incorrect(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
msgs = wf.add_input(wfmessages='string[]')
wf.validate()
with pytest.raises(ValueError):
wf.echo(message=msgs, scatter='message', scatter_method='blah')
def test_validate_with_inline_tools(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
wfmessage = wf.add_input(wfmessage='string')
echoed = wf.echo(message=wfmessage)
echoed2 = wf.echo(message=wfmessage)
wf.add_outputs(echoed2=echoed2)
wf.validate(inline=True)
def test_step_with_incompatible_step_output(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
infile = wf.add_input(infile='File')
wced = wf.wc(file2count=infile)
wf.validate()
with pytest.raises(ValueError):
echoed = wf.echo(message=wced)
def test_optional_to_optional_type(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
wf_infiles = wf.add_input(in_files='File[]')
wf_outdir = wf.add_input(out_dir='string?')
wf_counselors = wf.add_input(counselors='string[]')
out_files, meta_out = wf.multiple_out_args(
in_files=wf_infiles, out_dir=wf_outdir,
counselors=wf_counselors)
wf.validate()
def test_required_to_optional(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
# out_dir is optional, attaching to non-optional input
# should work.
wf_infiles = wf.add_input(in_files='File[]')
wf_outdir = wf.add_input(out_dir='string')
wf_counselors = wf.add_input(counselors='string[]')
out_files, meta_out = wf.multiple_out_args(
in_files=wf_infiles, out_dir=wf_outdir,
counselors=wf_counselors)
wf.validate()
def test_scatter_variable_correct(self):
scatter_methods = [
'dotproduct', 'nested_crossproduct', 'flat_crossproduct'
]
for method in scatter_methods:
wf = WorkflowGenerator()
wf.load('tests/data/tools')
msgs = wf.add_input(wfmessages='string[]')
echoed = wf.echo(
message=msgs, scatter='message', scatter_method=method)
wf.validate()
assert echoed.step_name == 'echo'
assert echoed.output_name == 'echoed'
def test_generate_step_name(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
wfmessage = wf.add_input(wfmessage='string')
name = wf._generate_step_name('echo')
echoed = wf.echo(message=wfmessage)
assert name == 'echo'
assert name == echoed.step_name
name = wf._generate_step_name('echo')
echoed2 = wf.echo(message=wfmessage)
assert name != 'echo'
assert name == echoed2.step_name
wf.validate()
